US20040067554A1

US20040067554A1 - Nucleotide sequences of moraxella catarrhalis genome

Info

Publication number: US20040067554A1
Application number: US10/672,787
Authority: US
Inventors: Robert Lagace; Chandra Patterson; Kim Berg
Original assignee: Lagace Robert E.; Chandra Patterson; Berg Kim L.
Current assignee: Merck and Co Inc
Priority date: 1999-06-18
Filing date: 2003-09-26
Publication date: 2004-04-08
Also published as: WO2000078968A2; EP1218512A2; CA2378687A1; US6632636B1; WO2000078968A3; AU1824101A

Abstract

The present invention provides the genomic sequences of a library of purified, polynucleotides, or their complements, comprising the genome of Moraxella catarrhalis. The invention also provides the identification of open reading frames contained within the polynucleotides of the library. The present invention further provides for the use of the polynucleotides, their complements or fragments, and proteins or portions thereof for identifying ligands and useful diagnostic and therapeutic compositions. In addition the invention provides for vectors, host cell sand methods for producing M. catarrhalis proteins or portions thereof.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No. 09/596,002, filed on Jun. 16, 2000, which claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application Serial No. 60/140,121, filed Jun. 18, 1999, both of which are hereby expressly incorporated herein by reference in their entireties.[0001]

A portion of the disclosure of this patent document contains material which is subject to copyright protection. The copyright owner has no objection to the facsimile reproduction by anyone of the patent document or the patent disclosure, as it appears in the Patent and Trademark Office patent file or records, but otherwise reserves all copyright rights whatsoever.

TECHNICAL FIELD

The present invention discloses nucleotide sequences from the genome of Moraxella catarrhalis. These sequences may be used in various assays and in the development of diagnostic and therapeutic agents.

Sequence Listing

The present application is being filed along with duplicate copies of a CD-ROM marked “Copy 1” and “Copy 2” containing a Sequence Listing in electronic format. The duplicate copies of the CD-ROM each contain a file entitled ELITRA.025C1.txt created on Sep. 26, 2003 which is 2,330,432 bytes in size. The information on these duplicate CD-ROMs is incorporated herein by reference in its entirety.

BACKGROUND OF INVENTION

All animals coexist with an indigenous microflora. Beginning shortly after birth, the gastrointestinal tract, lungs, and other areas of the human body are colonized by different bacterial species. A large number of factors operate to maintain symbiotic, host-microbe balance. These include the physical barriers of skin and mucosal surfaces and both nonspecific and highly specific aspects of the immune system. When host-microbe balance becomes disturbed, infection may ensue. Virulence, the ability of a microbe to produce infection, is related to a variety of complex mechanisms of disease induction. Some organisms are highly virulent and cause clinical illness when they colonize most or all hosts. Alternatively, when host defenses are compromised, normally symbiotic microbes can induce serious, or even life-threatening, infections. Thus, infection is generally a consequence of the interaction between a relatively virulent microbe and a normal host or between a relatively less virulent microbe and a host with some degree of transient or permanent immunological impairment.

M. catarrhalis (Branhamella catarrhalis) is a large, aerobic, gram-negative diplococcus normally found among the bacterial flora of human upper airways. It is nonmotile and possesses fimbriae. Collonies are regularly friable and nonadherent and grow well on blood or chocolate agar. Unlike many other pathogenic bacteria, M. catarrhalis shows a high degree of homogeneity in its outer membrane proteins. This usually harmless parasite of the mucous membranes may behave as an opportunistic pathogen when microbehost balance is perturbed. Following infection, host antibodies directed against one or more of the microbial outer-membrane proteins are detectable in the serum.

M. catarrhalis is known to cause acute, localized infections such as otitis media, sinusitis, and bronchopulmonary infection and life-threatening, systemic diseases including endocarditis and meningitis. The presence of bacterial endotoxin and host histamine and chemotactic factors are major indicators of M. catarrhalis pathogenicity.

M. catarrhalis can be isolated from the upper respiratory tract of 50% of healthy school children and 7% of healthy adults. In children with otitis media, colonization increases to 86%, and it is the third most common bacterial isolate. It causes 10-15% of otitis media and sinusitis. Infections of the maxillary sinuses, middle ears, or bronchi may occur through contiguous spread of the microbes. M. catarrhalis causes a large proportion of lower respiratory tract infections in elderly patients with chronic obstructive pulmonary diseases and is exceeded only by Haemoohilus influenzae and Streptococcus pneumoniae as a causative agent of acute purulent exacerbations of chronic bronchitis.

Pneumonia due to M. catarrhalis, like that of H. influenzae or S. pneumoniae, begins with aspiration of the bacteria. Failure or absence of appropriate host defense allows the bacteria to replicate and produce an inflammatory response in the alveoli. Because of mandatory immunosuppression, organ transplant recipients can develop moderate to severe M. catarrhalis pneumonia very rapidly. Bloodstream invasion is less characteristic of M. catarrhalis than pneumococcal infection, but nearly 50% of M. catarrhalis pneumonia patients die within 3 months of onset.

M. catarrhalis is treated with antibiotic agents including penicillin-clavulanic acid combinations, cephalosporins, tetracycline, erythromycin, chloramphenicol, trimethoprim-sulfamethoxazole, and quinolones. Over 85% of M. catarrhalis clinical isolates have been reported to be resistant to penicillin. Moreover, the microbe protects itself by binding to the first subcomponent of the complement system (Clq) which inactivates the C1 complex or by inactivating the terminal, lytic complement complex via a protein on the outer cell wall surface. Resistance is mediated by two closely related β-lactamases, BRO-1, present in 90% of resistant isolates and BRO-2, present in 10%. These enzymes are active against penicillin, ampicillin, and amoxicillin, less active against cephalosporins, and bind avidly to clavulanic acid and sublactam. Tetracycline resistant strains are increasing in Europe and Asia and have been documented in the United States. Ampicillin, which had been universally effective in treating M. catarrhalis pneumonia, can no longer be used.

M. catarrhalis physiology and pathogenicity are reviewed in: Holt et al. (1994) Bergey's Manual of Determinative Bacteriology, Williams and Wilkins, Baltimore Md.; Cullmann (1997) Med Klin 92(3):162-166; Isselbacher et al. (1994) Harrison's Principles of Internal Medicine, McGraw-Hill, New York N.Y.; Murray (1995) Manual of Clinical Microbiology, ASM Press, Washington D.C.; and Shulman et al. (1997) The Biologic and Clinical Basis of Infectious Diseases, W B Saunders, Philadelphia Pa.

In view of the conditions or diseases associated with M. catarrhalis, it would be advantageous to provide specific methods for the diagnosis, prevention, and treatment of diseases attributed to M. catarrhalis. Relevant methods would be based on the expression of M. catarrhalis-derived nucleic acid sequences. Such traits as virulence, acquisition of resistance factors, and effects of treatment using particular therapeutic agents may be characterized by under- or over-expression of nucleic acid sequences as revealed using PCR, hybridization or microarray technologies. Treatment for diseases attributed to M. catarrhalis can then be based on expression of these identified sequences or their expressed proteins, and efficacy of any particular therapy and development of resistance monitored. The information provided herein provides the basis for understanding the pathogenicity of M. catarrhalis and treating and monitoring the treatment of diseases caused by M. catarrhalis.

SUMMARY OF THE INVENTION

The present invention relates to a genomic library comprising the combination of nucleic acid molecules from Moraxella catarrhalis, presented as SEQ ID NOs:1-41. The library substantially provides the nucleic acid molecules comprising the genome of M. catarrhalis, and the nucleic acid molecules provide a plurality of open reading frames (ORFs). The ORFs uniquely identify structural, functional, and regulatory genes of M. catarrhalis. The invention encompasses oligonucleotides, fragments, and derivatives of the M. catarrhalis nucleic acid molecules, and sequences complementary to the nucleic acid molecules listed in the Sequence Listing.

M. catarrhalis nucleic acid molecules, fragments, derivatives, oligonucleotides, and complementary sequences thereof, can be used as probes to detect, amplify, or quantify M. catarrhalis genes, ORFs, cDNAs, or RNAs in biological, solution or substrate-based, assays or as compositions in diagnostic kits. The invention contemplates the use of such diagnostic probes to identify the presence of M. catarrhalis sequence in a sample or to screen for virulence factors and mutations.

The invention also provides for the comparison of the M. catarrhalis genomic library or the encoded proteins with genomes, individual DNA sequences, or proteins from other Moraxella species or strains, other bacteria, and other organisms to identify virulence factors, regulatory elements, drug targets, and to characterize genomic organization. In another aspect, the present invention provides for the use of computer databases to make such comparisons.

The invention further provides host cells and expression vectors comprising nucleic acid molecules of the invention and methods for the production of the proteins they encode. Such methods include culturing the host cells under conditions for expression of M. catarrhalis protein and recovering the protein from cell culture. The invention still further provides purified M. catarrhalis protein of which at least a portion is encoded by a nucleic acid molecule selected from the nucleic acid molecules of the Sequence Listing.

The subject invention provides a method of screening a library or a plurality of molecules or compounds for specific binding to a M. catarrhalis nucleic acid molecule or fragment thereof or protein or portion thereof, to identify at least one ligand which specifically binds the M. catarrhalis nucleic acid molecule or protein. Such a method comprises the steps of combining the M. catarrhalis nucleic acid molecule or protein with a library or a plurality of molecules or compounds under conditions to allow specific binding and detecting M. catarrhalis nucleic acid molecule or protein bound to at least one molecule or compound, thereby identifying a ligand which specifically binds the nucleic acid molecule or protein. Suitable libraries of ligands comprise aptamers, DNA molecules, RNA molecules, peptide nucleic acids, peptides, mimetics, proteins, agonists, antagonists, antibodies, inhibitors, immunoglobulins, pharmaceutical agents, and drug compounds.

The subject invention also provides a method of purifying a ligand from a sample. Such a method comprises the steps of combining the M. catarrhalis nucleic acid molecule or protein with a library or a plurality of molecules or compounds under conditions to allow specific binding, detecting M. catarrhalis nucleic acid molecule or protein bound to at least one molecule or compound, recovering the bound M. catarrhalis nucleic acid molecule or protein and separating the bound M. catarrhalis nucleic acid molecule or protein from the ligand, thereby obtaining purified ligand.

The invention further comprises an antibody specific for a purified M. catarrhalis protein or a portion thereof which is encoded by an M. catarrhalis nucleic acid molecule selected from the Sequence Listing. Antibodies produced against M. catarrhalis protein may be used diagnostically for the detection of M. catarrhalis proteins in biological, solution- or substrate-based, samples and therapeutically to neutralize the activity of an M. catarrhalis protein expressed during infections caused by M. catarrhalis.

DESCRIPTION OF THE SEQUENCE LISTING AND TABLES

The Sequence Listing is a compilation of the consensus sequences of contiguous sequences (contigs) or groups of overlapping sequences, assembled from individual sequences obtained by sequencing genomic clone inserts of a randomly generated M. catarrhalis DNA library. Each assembled contig or singlet is identified by a sequence identification number (SEQ ID NO) and by the contig number which it represents.

Table 1 lists the assembled M. catarrhalis contiguous sequences prepared as described in the Examples. The first column contains the number of the contig, which is also SEQ ID NO, listed in ascending order. The second column contains the length of the nucleic acid molecule. The third and fourth columns contain the start and stop nucleotides, respectively, for any open reading frames (ORFs) in the contig. The fifth column contains the Locus ID. The sixth column lists the GenBank identification number of the closest homolog, if any. The seventh column gives the P-value for the match to the homolog. The last column contains the description of the homolog. Orphans or LURs have no GenBank homologs.

Table 2 shows the order of the contigs or singlets comprising the M. catarrhalis genome.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

It is understood that this invention is not limited to the particular machines, materials and methods described. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to limit the scope of the present invention which will be limited only by the appended claims. As used herein, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. For example, a reference to “a host cell” includes a plurality of such host cells known to those skilled in the art.

All patents and publications cited for the purpose of describing and disclosing the cell lines, protocols, reagents and vectors which might be used in connection with the invention are expressly incorporated by reference. Citation is for the purpose of providing the best description of the invention and is not to be construed as an admission that the invention is not entitled to antedate such disclosure.

Definitions

“Biologically active” refers to a protein having structural, immunological, regulatory, or chemical functions of a naturally occurring, recombinant, or synthetic molecule.

“Complementary” refer to the natural hydrogen bonding by base pairing between purines and pyrimidines. For example, the sequence A-C-G-T forms hydrogen bonds with its complements T-G-C-A or U-G-C-A. The degree of complementarity between nucleic acid strands affects the efficiency and strength of the hybridization and amplification reactions.

“Derivative” refers to the chemical modification of a nucleic acid or amino acid molecule. Chemical modifications can include replacement of hydrogen by an alkyl, acyl, or amino group or glycosylation, pegylation, or any similar process which retains or enhances biological activity, stability, or lifespan of the molecule.

“Fragment” refers to an Incyte clone or any part of a nucleic acid molecule which retains a usable, functional characteristic. Useful fragments include oligonucleotides which may be used in hybridization or amplification technologies or to regulate replication, transcription or translation.

“Hybridization complex” refers to a complex between two nucleic acid molecules by virtue of the formation of hydrogen bonds between purines and pyrimidines.

“Ligand” refers to any molecule or compound which will bind to a complementary site on a nucleic acid molecule or protein.

“Modulates” refers to a change in activity (biological, chemical, or immunological) or lifespan resulting from specific binding between a molecule or compound and either a nucleic acid molecule or a protein.

“Molecules” is used substantially interchangeably with the terms agents and compounds. Such molecules modulate the activity of nucleic acid molecules or proteins of the invention and may be composed of at least one of the following: inorganic and organic substances including cofactors, nucleic acids, proteins, carbohydrates, fats, and lipids.

“Nucleic acid molecule” is substantially interchangeable with the term polynucleotide and may refer to a probe, a fragment of DNA or RNA of genomic or synthetic origin. Such molecules may be double-stranded or single-stranded and may be engineered into vectors to perform a particular activity such as transcription.

“Oligonucleotide” is substantially equivalent to the terms “amplimer”, “primer”, “oligomer”, and “element”, and is preferably single stranded.

“Protein” refers to an amino acid sequence, oligopeptide, peptide, polypeptide or portions thereof whether naturally occurring or synthetic.

“Portion” refers to any part of a protein used for any purpose, but especially for the screening of a library of molecules or compounds which specifically bind to that portion or for the production of antibodies.

“Sample” is used in its broadest sense. A sample containing nucleic acid molecules may comprise a bodily fluid; an extract from a cell, chromosome, organelle, or membrane isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; a cell; a tissue; a tissue print; a hair, and the like.

“Substantially purified” refers to nucleic acid molecules or proteins that are isolated or separated from their natural environment and are about 60% free to about 90% free from other components with which they are naturally associated.

“Substrate” refers to any rigid or semi-rigid support to which nucleic acid molecules or proteins are bound and includes membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, capillaries or other tubing, plates, polymers, and microparticles with a variety of surface forms including wells, trenches, pins, channels and pores.

The Invention

The majority of the Moraxella catarrhalis genome was sequenced using a strategy of shotgun sequencing. Genomic DNA was mechanically sheared, treated with enzyme to create blunt ends, gel-purified, and cloned into modified PBLUESCRIPT vectors (Stratagene, La Jolla Calif.). The vectors were transformed into E. coli cells and grown overnight. Colonies were picked, and plasmid DNA was isolated. Templates were prepared and sequenced, sequences were assembled into contiguous sequences (contigs), and open reading frames were identified.

The invention relates to a Moraxella catarrhalis genomic DNA library comprising a combination of nucleic acid molecules, SEQ ID NOs:1-41, and their complements. These nucleic acid molecules comprise contiguous sequences which contain annotated and unannotated reading frames (ORFs and LURs). The nucleic acid molecules or fragments and probes thereof are used in hybridization, screening, and purification assays to identify ligands and in vectors and host cells to produce the proteins which they encode. The proteins or portions thereof are also used in screening and purification assays to identify useful ligands or to produce antibodies. The molecules or compounds used in hybridization, screening, and purification assays include aptamers, DNA molecules, RNA molecules, peptide nucleic acids, peptides, mimetics, transcription factor, enhancers, repressors, regulatory proteins, agonists, antagonists, antibodies, inhibitors, immunoglobulins, pharmaceutical agents, drug compounds, and the like. The nucleic acid molecules and proteins of M. catarrhalis are compared with those of other organisms using computer algorithms and databases to select those nucleic acid molecules and proteins of potential diagnostic and therapeutic use.

Characterization and Use of the Invention

Sequencing

Methods for sequencing nucleic acid molecules are well known in the art and may be used to practice any of the embodiments of the invention. These methods employ enzymes such as the Klenow fragment of DNA polymerase I, SEQUENASE, Taq DNA polymerase, thermostable T7 DNA polymerase (Amersham Pharmacia Biotech (APB), Piscataway N.J.), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies, Rockville Md.). Preferably, sequence preparation is automated with machines such as the HYDRA microdispenser (Robbins Scientific, Sunnyvale Calif.), MICROLAB 2200 system (Hamilton, Reno Nev.), and the DNA ENGINE thermal cycler (MJ Research, Watertown Mass.). Machines used for sequencing include the ABI 3700, 377 or 373 DNA sequencing systems (PE Biosystems, Foster City Calif.), the MEGABACE 1000 DNA sequencing system (APB), and the like. The sequences may be analyzed using a variety of algorithms which are well known in the art and described in Ausubel (1997 ; Short Protocols in Molecular Biology, John Wiley & Sons, New York N.Y., unit 7.7) and in Meyers (1995; Molecular Biology and Biotechnology, Wiley VCH, New York N.Y., pp. 856-853).

Shotgun sequencing methods are well known in the art and use thermostable DNA polymerases and heat-labile DNA polymerases. A detailed procedure is provided in the Examples. Prefinished sequences (incomplete assembled sequences) are cross-compared for identity using various algorithms or programs such as CONSED (Gordon (1998) Genome Res. 8:195-202), GELVIEW Fragment Assembly system (Genetics Computer Group, Madison Wis., and PHRAP (Phil Green, University of Washington, Seattle Wash.). Contaminating sequences, including vector or chimeric sequences, can be masked, removed or restored, in the process of turning the prefinished sequences into finished sequences.

Extension of a Nucleic Acid Sequence

The sequences of the invention may be extended using various PCR-based methods known in the art. For example, the XL-PCR kit (PE Biosystems), nested primers, and commercially available cDNA or genomic DNA libraries (Life Technologies and Clontech (Palo Alto Calif.), respectively) may be used to extend the nucleic acid sequence. For all PCR-based methods, primers may be designed using commercially available software, such as OLIGO 4.06 software (National Biosciences, Plymouth Minn.) to be about 22 to 30 nucleotides in length, to have a GC content from about 40-45%, and to anneal to a target molecule at temperatures from about 55 C to about 68 C. When extending a sequence to recover untranslated, regulatory elements, it is preferable to use genomic, rather than cDNA libraries.

Use of M. catarrhalis Nucleic Acid Molecules

Hybridization

The M. catarrhalis nucleic acid molecules and fragments thereof can be used in various hybridization technologies for various purposes. Hybridization probes may be designed or derived from a highly unique region such as the 5′ untranslated sequence preceding the initiation codon or from a conserved coding region encoding a specific protein signature or motif and used in protocols to identify naturally occurring molecules encoding a particular M. catarrhalis protein, allelic variants, or related molecules. The probe should preferably have at least 50% sequence identity to any naturally occurring nucleic acid sequences. The probe may be a single stranded DNA or RNA molecule, produced biologically or synthetically, and labeled using oligolabeling, nick translation, end-labeling, or PCR amplification in the presence of at least one labeled nucleotide. A vector containing the nucleic acid molecule or a fragment thereof may be used to produce an mRNA probe in vitro by addition of an RNA polymerase and labeled nucleotides. These procedures may be conducted using commercially available kits such as those provided by APB.

The stringency of hybridization is determined by G+C content of the probe, salt concentration, and temperature. In particular, stringency can be increased by reducing the concentration of salt or raising the hybridization temperature. In solutions used for some membrane based hybridizations, addition of an organic solvent such as formamide allows the reaction to occur at a lower temperature. Hybridization can be performed at low stringency with buffers, such as 5×SSC with 1% sodium dodecyl sulfate (SDS) at 60 C, which permits the formation of a hybridization complex between nucleic acid sequences that contain some mismatches. Subsequent washes are performed at increased stringency with buffers such as 0.2×SSC with 0.1% SDS at either 45 C (medium stringency) or 68 C (high stringency). At high stringency, hybridization complexes will remain stable only where the nucleic acid molecules are completely complementary. In some membrane-based hybridizations, 35-50% formamide can be added to the hybridization solution to reduce the temperature at which hybridization is performed. Background signals can be reduced by the use of other detergents such as Sarkosyl or TRITON X-100 (Sigma-Aldrich, St. Louis Mo.) and a blocking agent such as denatured salmon sperm DNA. Selection of components and conditions for hybridization are well known to those skilled in the art and are reviewed in Ausubel (supra) and in Sambrook et al. (1989 ; Molecular Cloning A Laboratory Manual, Cold Spring Harbor Press, Plainview N.Y.).

Microarrays may be prepared and analyzed using methods known in the art. Oligonucleotides or fragments of a nucleic acid molecule may be used as either probes or targets. The microarray can be used to monitor the expression level of large numbers of genes simultaneously and to identify genetic variants, mutations, and single nucleotide polymorphisms. Such information may be used to determine gene function; to understand the genetic basis of a condition, disease, or disorder; to diagnose a condition, disease, or disorder; and to develop and monitor the activities of therapeutic agents used to treat the condition, disease, or disorder. (See, eg, Brennan et al. (1995) U.S. Pat. No. 5,474,796; Schena et al. (1996) Proc Natl Acad Sci 93:10614-10619; Baldeschweiler et al. (1995) PCT application WO95/251116; Shalon et al. (1995) PCT application WO95/35505; Heller et al. (1997) Proc Natl Acad Sci 94:2150-2155; and Heller et al. (1997) U.S. Pat. No. 5,605,662.)

Hybridization probes are also useful in mapping the naturally occurring genomic sequence. The probes may be hybridized to: 1) a particular chromosome, 2) a specific region of a chromosome, 3) an artificial chromosome constructions such as human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial PI constructions, single chromosomes from eukaryotic species, or 5) DNA libraries made from any of these sources.

Expression

A nucleic acid molecule encoding a M. catarrhalis protein may be cloned into a vector and used to express the protein or portions thereof in host cells. The nucleic acid sequence can be engineered by such methods as DNA shuffling (U.S. Pat. No. 5,830,721) and site-directed mutagenesis to create new restriction sites, alter glycosylation patterns, change codon preference to increase expression in a particular host, produce splice variants, extend half-life, and the like. The expression vector may contain transcriptional and translational control elements (promoters, enhancers, specific initiation signals, and polyadenylated sequence) from various sources which have been selected for their efficiency in a particular host. The vector, nucleic acid molecule, and regulatory elements are combined using in vitro recombinant DNA techniques, synthetic techniques, and/or in vivo genetic recombination techniques well known in the art and described in Sambrook (supra ch. 4, 8, 16 and 17).

A variety of host systems may be transformed with an expression vector. These include, but are not limited to, bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems transformed with baculovirus expression vectors; plant cell systems transformed with expression vectors containing viral and/or bacterial elements, or animal cell systems (Ausubel, supra, unit 16).

Routine cloning, subcloning, and propagation of nucleic acid molecules can be achieved using the multifunctional PBLUESCRIPT vector (Stratagene) or PSPORT1 plasmid (Life Technologies). Introduction of a nucleic acid sequence into the multiple cloning site of these vectors disrupts the lacZ gene and allows colorimetric screening for transformed bacteria. In addition, these vectors may be useful for in vitro transcription, dideoxy sequencing, single strand rescue with helper phage, and creation of nested deletions in the cloned sequence.

For long term production of recombinant M. catarrhalis proteins, the vector can be stably transformed into competent cells of E. coli along with a selectable or visible marker gene on the same or on a separate vector. After transformation, cells are allowed to grow in enriched media containing a selective agent. Selectable markers, antimetabolite, antibiotic, or herbicide resistance genes confer resistance to the respective selective agent and allow growth and recovery of cells which successfully express the introduced sequences. Resistant clones or colonies, identified either by survival on selective media or by the expression of visible markers, such as anthocyanins, green fluorescent protein (GFP), β glucuronidase, luciferase and the like, may be propagated using culture techniques well known in the art. Visible markers are also used to quantify the amount of protein expressed by the introduced genes. Verification that the host cell contains the desired M. catarrhalis nucleic acid molecule is based on DNA-DNA or DNA-RNA hybridizations or PCR amplification.

The host cell may be chosen for its ability to modify a recombinant protein in a desired fashion. Such modifications include acetylation, carboxylation, glycosylation, phosphorylation, lipidation, acylation, and the like. Post-translational processing sequences (“prepro” forms) may also be engineered into the recombinant nucleotide sequence in order to specify protein targeting, folding, and/or activity. Different host cells available from the ATCC (Manassas Va.) which have specific cellular machinery and characteristic mechanisms for post-translational activities may be chosen to ensure the correct modification and processing of the recombinant protein.

Recovery of Proteins from Cell Culture

Heterologous moieties engineered into a vector for ease of purification include glutathione S-transferase (GST), calmodulin binding peptide (CBP), 6×His, FLAG, MYC, and the like. GST, CBP, and 6×His are purified using commercially available affinity matrices such as immobilized glutathione, calmodulin, and metal-chelate resins, respectively. FLAG and MYC are purified using commercially available monoclonal and polyclonal antibodies. A proteolytic cleavage site may be located between the desired protein sequence and the heterologous moiety for ease of separating the desired protein following purification. Methods for recombinant protein expression and purification are discussed in Ausubel (supra, unit 16) and are commercially available (Invitrogen, San Diego Calif.).

Chemical Synthesis of Peptides

Proteins or portions thereof may be produced not only by recombinant methods, but also by using chemical methods well known in the art. Solid phase peptide synthesis may be carried out in a batchwise or continuous flow process which sequentially adds α-amino and side chain-protected amino acid residues to an insoluble polymeric support via a linker group. A linker group such as methylamine-derivatized polyethylene glycol is attached to poly(styrene-co-divinylbenzene) to form the support resin. The amino acid residues are N-α-protected by acid labile Boc (t-butyloxycarbonyl) or base-labile Fmoc (9-fluorenylmethoxycarbonyl). The carboxyl group of the protected amino acid is coupled to the amine of the linker group to anchor the residue to the solid phase support resin. Trifluoroacetic acid or piperidine are used to remove the protecting group in the case of Boc or Fmoc, respectively. Each additional amino acid is added to the anchored residue using a coupling agent or pre-activated amino acid derivative, and the resin is washed. The full length peptide is synthesized by sequential deprotection, coupling of derivitized amino acids, and washing with dichloromethane and/or N,N-dimethylformamide. The peptide is cleaved between the peptide carboxy terminus and the linker group to yield a peptide acid or amide. (Novabiochem 1997/98 Catalog and Peptide Synthesis Handbook, San Diego Calif., pp. S1-S20). Automated synthesis may also be carried out on machines such as the ABI 431A peptide synthesizer (PE Biosystems). A protein or portion thereof may be substantially purified by preparative high performance liquid chromatography and its composition confirmed by amino acid analysis or by sequencing (Creighton (1984) Proteins, Structures and Molecular Properties, W H Freeman, New York N.Y.).

Preparation and Screening of Antibodies

Various hosts including goats, rabbits, rats, mice, humans, and others may be immunized by injection with M. catarrhalis protein or any portion thereof. Adjuvants such as Freund's, mineral gels, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemacyanin (KLH), and dinitrophenol may be used to increase immunological response. The oligopeptide, peptide, or portion of protein used to induce antibodies should consist of about five to fifteen amino acids which are identical to a portion of the natural protein. Oligonucleotides may be fused with proteins such as KLH in order to produce antibodies to the chimeric molecule.

Monoclonal antibodies may be prepared using any technique which provides for the production of antibodies by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique. (See, eg, Kohler et al. (1975) Nature 256:495-497; Kozbor et al. (1985) J Immunol Methods 81:31-42; Cote et al. (1983) Proc Natl Acad Sci 80:2026-2030; and Cole et al. (1984) Mol Cell Biol 62:109-120.)

Alternatively, techniques described for the production of single chain antibodies may be adapted, using methods known in the art, to produce epitope specific single chain antibodies. Antibody fragments which contain specific binding sites for epitopes of the M. catarrhalis protein may also be generated For example, such fragments include, but are not limited to, F(ab′)₂fragments produced by pepsin digestion of the antibody molecule and Fab fragments generated by reducing the disulfide bridges of the F(ab′)₂fragments. Alternatively, Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity (Huse et al. (1989) Science 246:1275-1281).

The M. catarrhalis protein may be used in screening assays of phage mid or B-lymphocyte immunoglobulin libraries to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoassays using either polyclonal or monoclonal antibodies with established specificities are well known in the art. Such immunoassays typically involve the measurement of complex formation between the protein and its specific antibody. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes is preferred, but a competitive binding assay may also be employed (Pound (1998) Immunochemical Protocols, Humana Press, Totowa N.J.).

Labeling of Molecules for Assay

A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid molecule, protein, and antibody assays. Synthesis of labeled molecules may be achieved using Promega (Madison Wis.) or APB kits for incorporation of a labeled nucleotide such as ³²p-dCTP, Cy3-dCTP or Cy5dCTP (APB) or amino acid such as ³⁵S-methionine (APB). Nucleotides and amino acids may be directly labeled with a variety of substances including fluorescent, chemiluminescent, or chromogenic agents and the like, by chemical conjugation to amines, thiols and other groups present in the molecules using reagents such as BIODIPY or FITC (Molecular Probes, Eugene Oreg.).

Diagnostics

The nucleic acid molecules, fragments, oligonucleotides, complementary RNA and DNA molecules, and peptide nucleic acids (PNAs) may be used to detect and quantify differential gene expression, absence/presence vs. excess, of mRNAs or to monitor mRNA levels following drug treatment. Conditions, diseases or disorders associated with M. catarrhalis gene expression may include conditions and diseases such as allergies, asthma, bronchitis, chronic obstructive pulmonary disease, emphysema, endocarditis, hypereosinophilia, meningitis, otitis media, pneumonia, sinusitis, and various respiratory distress syndromes. The diagnostic assay may use hybridization or amplification technology to compare gene expression in a biological sample from a patient to expression in disease and control standards in order to detect differential gene expression. Qualitative or quantitative methods for this comparison are well known in the art.

For example, the nucleic acid molecule, fragment, or probe may be labeled by standard methods and added to a sample from a patient under conditions for the formation of hybridization complexes. After an incubation period, the sample is washed and the amount of label (or signal) associated with hybridization complexes, is quantified and compared with a standard value. If the amount of label in the patient sample is significantly altered in comparison to the standard value, then the presence of elevated amounts of M. catarrhalis is responsible for the associated condition or disease.

In order to provide a basis for the diagnosis of a condition, disease or disorder associated with gene expression, a normal or standard expression profile is established. This may be accomplished by combining a biological sample taken from normal subjects, animal or more preferably human, with a probe under conditions for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained using normal subjects with values from an experiment in which a known amount of a substantially purified target sequence is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who are symptomatic for a particular condition or diseases listed above. Deviation from standard values toward those associated with a particular diagnosed condition is used to diagnose the patient.

Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies or in a clinical trial. Once efficacy is established, these assays may be used on a regular basis to determine if the therapy is effective in an individual patient. The results obtained from successive patient assays may be used over a period ranging from several days to months.

Immunological Methods

Detection and quantification of a protein using either specific polyclonal or monoclonal antibodies are known in the art. Examples of such techniques include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays, and fluorescence activated cell sorting. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes is preferred, but a competitive binding assay may be employed. (See, eg, Coligan et al. (1997) Current Protocols in Immunology, Wiley-Interscience, New York N.Y.; Pound, supra.)

Therapeutics

Chemical and structural similarity, in the context of sequences, signatures and motifs, antigenic epitopes and the like, generally exists between regions of homologous proteins. Comparisons of M. catarrhalis nucleic acid molecules and proteins with those of other M. catarrhalis strains, other bacteria and other organisms allow preselection of therapeutic agents that affect the pathogenic organism without harming the host. Such therapeutic agents are useful in treating conditions and diseases such as allergies, asthma, bronchitis, chronic obstructive pulmonary disease, emphysema, endocarditis, hypereosinophilia, meningitis, otitis media, pneumonia, sinusitis, and various respiratory distress syndromes caused by M. catarrhalis. In conditions associated with increased expression or activity of M. catarrhalis nucleic acid molecule or protein, it is desirable to decrease expression or protein activity.

In one embodiment, a ligand such as an antagonist, antibody, or inhibitor identified by screening a plurality of molecules with the M. catarrhalis protein is administered to the subject to decrease the activity of the M. catarrhalis or homologous protein as it is overexpressed during pathogenesis.

In another embodiment, a composition comprising the substantially purified ligand and a pharmaceutical carrier may be administered to a subject to decrease the activity of the M. catarrhalis or homologous protein as it is overexpressed during pathogenesis. In one aspect, an antibody which specifically binds the M. catarrhalis protein may be used as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissues which are affected by the overexpression of the M. catarrhalis protein.

Any of the ligands may be administered in combination with other therapeutic agents. Selection of the agents for use in combination therapy may be made by one of ordinary skill in the art according to conventional pharmaceutical principles. A combination of therapeutic agents may act synergistically to effect prevention or treatment of a particular condition at a lower dosage of each agent.

Modification of Gene Expression Using Nucleic Acids

Gene expression may be modified by designing complementary or antisense molecules (DNA, RNA, or PNA) to the 5′, 3′, or intronic regions of the M. catarrhalis nucleic acid molecule. Oligonucleotides designed with reference to the transcription initiation site are preferred. Similarly, inhibition can be achieved using triple helix base-pairing which inhibits the binding of polymerases, transcription factors, or regulatory molecules (Gee et al. In: Huber and Carr (1994) Molecular and Immunologic Approaches, Futura Publishing, Mt. Kisco N.Y., pp. 163-177). A complementary molecule may also be designed to block translation by preventing binding between ribosomes and mRNA. In one alternative, a library of cDNA molecules may be screened to identify those which specifically bind a regulatory, untranslated M. catarrhalis sequence. Delivery of this inhibitory nucleotide sequence using a vector designed to be transferred from transformed M. catarrhalis cells to infectious M. catarrhalis via genetic recombination is contemplated.

Ribozymes, enzymatic RNA molecules, may also be used to catalyze the specific cleavage of an M. catarrhalis RNA. The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA followed by endonucleolytic cleavage at sites such as GUA, GUU, and GUC. Once such sites are identified, an oligonucleotide with the same sequence may be evaluated for secondary structural features which would render the oligonucleotide inoperable. The suitability of candidate targets may also be evaluated by testing their hybridization with complementary oligonucleotides using ribonuclease protection assays.

Complementary nucleic acids and ribozymes of the invention maybe prepared via recombinant expression, in vitro or in vivo, or using solid phase phosphoramidite chemical synthesis. In addition, RNA molecules may be modified to increase intracellular stability and half-life by addition of flanking sequences at the 5′ and/or 3′ ends of the molecule or by the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. Modification is inherent in the production of PNAs and can be extended to other derivative nucleotide molecules. Either the inclusion of nontraditional bases such as inosine, queosine, and wybutosine, and/or the modification of adenine, cytidine, guanine, thymine, and uridine with acetyl-, methyl-, thio-groups renders the molecule less available to endogenous bacterial endonucleases.

Screening Assays

The M. catarrhalis nucleic acid molecule may be used to screen a plurality or a library of molecules or compounds for specific binding affinity. The molecules or compounds may be selected from aptamers, DNA molecules, RNA molecules, PNAs, peptides, transcription factors, enhancers, repressors, regulatory proteins and other ligands which modulate the activity, replication, transcription, or translation of the nucleic acid molecules in the biological system. The assay involves combining the M. catarrhalis nucleic acid molecule or a fragment thereof with molecules or compounds under conditions to allow specific binding, and detecting specific binding to identify at least one ligand which specifically binds the M. catarrhalis nucleic acid molecule.

Similarly the M. catarrhalis protein or a portion thereof may be used to screen a plurality of libraries of molecules or compounds in any of a variety of screening assays. The molecules or compounds may be selected from aptamers, DNA molecules, RNA molecules, peptide nucleic acids, peptides, mimetics, proteins, agonists, antagonists, antibodies, inhibitors, immunoglobulins, pharmaceutical agents, drug compounds, and the like. The protein or portion thereof employed in such screening may be free in solution, affixed to an abiotic or biotic substrate (eg, borne on a cell surface), or located intracellularly. Specific binding between the protein and molecule may be measured. One method for high throughput screening using very small assay volumes and very small amounts of test compound is described in U.S. Pat. No. 5,876,946, incorporated herein by reference, which teaches how to screen large numbers of molecules for specific binding to a protein.

Purification of Ligand

The M. catarrhalis nucleic acid molecule or a fragment thereof may be used to purify a ligand from a sample. A method for using a M. catarrhalis nucleic acid molecule or a fragment thereof to purify a ligand would involve combining the nucleic acid molecule or a fragment thereof with a sample under conditions to allow specific binding, detecting specific binding, recovering the bound M. catarrhalis nucleic acid molecule, and using an appropriate agent to separate the M. catarrhalis nucleic acid molecule from the purified ligand.

Similarly, the protein or a portion thereof may be used to purify a ligand from a sample. A method for using a M. catarrhalis protein or a portion thereof to purify a ligand would involve combining the protein or a portion thereof with a sample under conditions to allow specific binding, detecting specific binding between the protein and ligand, recovering the bound protein, and using an appropriate chaotropic agent to separate the protein from the purified ligand.

Pharmacology

Pharmaceutical compositions are those substances wherein the active ingredients are contained in an effective amount to achieve a desired and intended purpose. The determination of an effective dose is well within the capability of those skilled in the art. For any compound, the therapeutically effective dose may be estimated initially either in cell culture assays or in animal models. The animal model is also used to achieve a desirable concentration range and route of administration. Such information may then be used to determine useful doses and routes for administration in humans.

A therapeutically effective dose refers to that amount of a pharmaceutical agent which ameliorates the symptoms or condition. Therapeutic efficacy and toxicity of such agents may be determined by standard pharmaceutical procedures in cell cultures or experimental animals, eg, ED ₅₀(the dose therapeutically effective in 50% of the population) and LD₅₀(the dose lethal to 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index, and it may be expressed as the ratio, LD₅₀/ED₅₀. Pharmaceutical compositions which exhibit large therapeutic indexes are preferred. The data obtained from cell culture assays and animal studies are used in formulating a range of dosage for human use.

Rational Drug Design

The goal of rational drug design is to produce structural analogs of biologically active M. catarrhalis proteins of interest or of ligands with which they interact. Any of these examples can be used to fashion drugs which are more active or stable forms of the protein, or which enhance or interfere with the function of a protein in vivo (Hodgson (1991) Bio/Technology 9:19-21).

In one approach, the three-dimensional structure of an M. catarrhalis protein, or of an M. catarrhalis protein-inhibitor complex, is determined by X-ray crystallography, by computer modeling or, most typically, by a combination of the two approaches. Both the shape and charges of the protein must be ascertained to elucidate the structure and to determine active site(s). Less often, useful information regarding the structure of a protein may be gained by modeling based on the structure of homologous proteins. In both cases, relevant structural information is used to design analogous M. catarrhalis protein-like molecules or to identify efficient inhibitors.

Useful examples of rational drug design may include molecules which have improved activity or stability, as shown by Braxton et al. (1992 , Biochem 31:77967801), or which act as inhibitors, agonists, or antagonists of M. catarrhalis peptides, as shown by Athauda et al. (1993, J Biochem 113:742-746).

It is also possible to isolate a target-specific antibody, selected by functional assay, as described above, and then to solve its crystal structure. This approach, in principle, yields a pharmacore upon which subsequent drug design can be based. It is possible to bypass protein crystallography altogether by generating anti-idiotypic antibodies (anti-ids) to a functional, pharmacologically-active antibody. As a mirror image of a mirror image, the binding site of the anti-id is an analog of the original receptor. The anti-id can be used to identify and isolate peptides from banks of chemically or biologically-produced peptides. The isolated peptides act as the pharmacore.

EXAMPLES

Example 1

Shotgun Sequencing Strategy

The strategy for sequencing the [0103] M. catarrhalis genome was a modification of the shotgun approach to whole genome sequencing described by Lander and Waterman (1988 Genomics 2:231). They applied the equation for the Poisson distribution p_x=m^xe^−m/x!, where x is the number of occurrences of an event, m is the mean number of occurrences, and P_xis the probability that any given base is not sequenced after a certain amount of random sequence has been generated. If L is the genome length, n is the number of clones insert ends sequenced, and w is the sequencing read length, then m=nw/L, and the probability that no clone originates at any of the w bases preceding a given base, ie, the probability that a base is not sequenced, is p₀=e^−m. For sequencing where p₀>0, the total gap length is Le^−m, and the average gap size is L/n.
The shotgun approach has recently been used to sequence the genomes of [0104] H. influenzae (Fleischmann et al. (1995) Science 269:496; WO 96/33276), Mycoplasma genitalium (Fraser et al. (1995) Science 270:397 and Methanococcus jannashii (Bult et al. (1996) Science 273:1058). All of these microbes have relatively small genomes of 1.8, 0.6, and 1.8 megabases, respectively. The size of the M. catarrhalis genome is estimated to be 1.9 megabases.

Example 2

Construction of the Genomic Library

An [0105] M. catarrhalis genomic DNA library was constructed using DNA purified from the gram negative, aerobic diplococcus, M. catarrhalis, ATCC accession number 43617. The isolate was obtained from transtracheal aspirate of a coal miner with chronic bronchitis. The G+C content is 42%.
Using a syringe fitted with a 0.0025 in. Ruby orifice (Stanford University, Stanford Calif.), 50 μg of [0106] M. catarrhalis DNA was sheared into 1.5-2.9 kb fragments. The shearing process was monitored by electrophoresis of a subsample of sheared DNA on a 0.8% SEAKEM GTG agarose gel (FMC Bioproducts, Rockland Me.) in 1×TAE buffer at about 950 V-h. Comparison with a DNA ladder with known size fragments was used to verify the size and quality of the sheared DNA
Sheared DNA was visualized with low wavelength UV and bands of 1.5 to 2.8 kbs were removed from a preparative 0.8% SEAKEM GTG agarose gel (FMC Bioproducts). The 1.5-2.9 kb fragments were electrophoresced through a preparative 0.8% SEAPLAQUE GTG low melt agarose gel (FMC Bioproducts) in 1×TAE buffer at about 850 V-h. The DNA band was removed from the low melt agarose, placed in an microcentrifuge tube, and the agarose melted at 65 C for 10-15 minutes. After 5 minutes of heating, the melted agarose was diluted with a half volume of double distilled water, and the sample was equilibrated to 42 C. β-AGARASE (New England Biolabs (NEB), Beverly Mass.) and 10xβ-AGARASE (NEB) were added, and the preparation was incubated for 1-3 hours with addition of a half initial volume of β-AGARASE (NEB) after 1 hour and mixing by inversion every half hour. The DNA was extracted once with phenol:chloroform:isoamyl alcohol (25:24:1) followed by extraction with chloroform:isoamyl alcohol (24:1) and precipitated by addition of 1-3 μl glycogen, {fraction (1/10)} volume 3M NaOAc, and 2.5 volumes cold 100% ethanol. The sample was stored overnight at −20 C. [0107]
The purified DNA strands were treated with BAL31 (NEB) at 1 U/20 μg DNA in a final volume of 50 μl at 30 C for 10 minutes to prepare blunt ends. Then the DNA was re-extracted as above (phenol:chloroform:isoamyl alcohol followed by chloroform:isoamyl alcohol). The DNA was reprecipitated as above and stored at −20 C until ligation into the vector. [0108]
The PBLUESCRIPT plasmid (Stratagene) was cut with SmaI endonuclease, and the ends of the strands dephosphorylated to prepare the BS.S2 vector. The purified [0109] M. catarrhalis DNA (2 μg) was ligated into the BS.S2 vector (1 μg) with T4 DNA ligase (Life Technologies) for 4 hours at 14 C. Following the ligation reaction, the ligated DNA was extracted and precipitated as above. The ligated vector:insert DNA was the size selected (vector+insert=4.4-5.7 kb) and purified by gel electrophoresis and extracted as described above.
Following gel purification, the ends of the vector:insert DNA were repaired using T4 DNA polymerase (NEB) for 5 minutes at 37 C, re-extracted and precipitated as above, and self-ligated into circles with T4 DNA ligase (Life Technologies). After 10 minutes, the ligation reaction was stopped by heating at 70 C for 10 minutes. [0110]
The circular plasmid was transformed into DH10B competent cells (Life Technologies) by electroporation at 1.8 volts. Transformed cells were selected by growth on X-Gal+isopropyl beta-D-thiogalactopyranoside (IPTG)+2× carbenicillin (carb) LB agar plates. [0111]

Example 3

Isolation of Clones and Sequencing

Plasmid DNA was released from the cells and purified using the REAL PREP 96 plasmid kit (QIAGEN, Chatsworth Calif.). This kit enabled simultaneous purification of 96 samples in a 96-well block using multi-channel reagent dispensers. The recommended protocol was employed except for the following changes: 1) the bacteria were cultured in 1 ml of sterile TERRIFIC BROTH (BD Biosciences, Sparks Md.) with carb at 25 mg/l and glycerol at 0.4%; 2) after inoculation and incubation for 19 hours, the cells were lysed with 0.3 ml of lysis buffer; and 3) following isopropanol precipitation, the plasmid DNA pellet was resuspended in 0.1 ml of distilled water. After this final step, samples were transferred to a 96-well block for storage at 4 C. [0112]
The DNA inserts were prepared for sequencing using a 96 well HYDRA microdispenser (Robbins Scientific) in combination with DNA ENGINE thermal cyclers (MJ Research). After thermal cycling, the A, C, G, and T reactions with each DNA template were combined. Then, 50 μl 100% ethanol was added, and the solution was spun at 4 C for 30 min at 4500 rpm in a centrifuge (Jouan, Winchester Va.). After the pellet was dried for 15 min under vacuum, the DNA sample was dissolved in 3 μl of formaldehyde/50 mM EDTA and loaded on wells in volumes of 1 μl per well for sequencing. Sequencing used the method of Sanger and Coulson (1975, J. Mol. Biol. 94:441f) and an ABI PRISM 377 sequencing systems (PE Biosystems). After electrophoresis for four hours on 4% acrylamide gels on 36 cm plates at 2.3 kV, approximately 500-650 bps were determined per sequence. [0113]

Example 4

Sequence Processing and Contiguous Sequence Assembly

Sequences were generated from either shotgun sequencing or closure sequencing. Closure sequences were obtained by directed genomic walks or PCR of specific genomic regions. In the latter case, the PCR products were sequenced. [0114]
Sequences were edited in a two-step process. In the first step, vector sequences from both the 5′ and 3′ ends were clipped using the algorithm provided in U.S. Ser. No. 09/276,534 filed Mar. 25, 1999. In the second step, possible contaminating sequence was removed by reading each raw sequence and performing a cross-match search against a contamination database containing known vector sequences and DNA marker sequences. Sequences with cross-match scores of 18 or greater were removed. [0115]
Contigs were assembled using PHRAP (Green, supra) which aligns multiple, overlapping DNA sequences to form a contiguous consensus sequence. Alignments were influenced by quality scores assigned to each base in a sequence. A single sequence cannot belong to more than one contig. [0116]
The 41 contigs presented in Table 1 and the Sequence Listing were assembled from 47385 individual sequences. The contigs represent approximately 13.3× coverage or 100.7% of the [0117] M. catarrhalis genome.

Example 5

Gene Finding

ORF identification was carried out through combination of BLAST (Karlin, supra) and FASTA searches. These serial searches compared the consensus sequences of the assembled contigs, presented in Table 1, against sequences in public-domain databases. The searches identified similarity matches, or “hits”, that indicated an ORF within the sequence. [0118]
The consensus sequences of the contigs were analyzed against the GenBank peptide (GenPept) database. The ORF identification process assigned ORFs to loci on a contig. If a match was found at a P-value less than or equal to 1e-6, the corresponding locus on the contig was designated as an ORF. This portion of the contig was masked by Ns, and the consensus sequence underwent a second BLASTX or FASTX search against the GenPept database. Again, the match with the lowest P-value (less than or equal to 1e-6) was used to identify a second ORF. The corresponding sequences were masked, and the process continued until all BLASTX and FASTX matches with P-values less than or equal to le-6 had been identified for a given contig. Then, the contigs were run through GeneMark, an algorithm for identifying putative ORFs. The GeneMark algorithm is described and developed in the following references: Borodovsky and McIninch (1993) Computers & Chemistry 17:123; Blattner et al. (1993) Nucl Acid Res 21:5408; and Borodovsky et al. (1994) Trends Biochem Sci 19:309. After all possible homology and algorithm-based ORFs were identified, a process called ORF selection was applied. In this process GeneMark ORFs that overlapped homology-based ORFs were rejected, and homology-based ORFs were retained. GeneMark ORFs that did not overlap homology-based ORFs and those that overlapped other GeneMark ORFs were retained. Finally, all ORFs were annotated by performing BLAST2 comparisons against GenPept and taking annotation from the best hit with P-value less than or equal to 1e-6. [0119]
Contigs with high probability for ORFs, but no identified ORFs, were identified as “orphan” contigs (Table 1). Unannotated regions of contigs exceeding 500 bases in length were identified as “Long-Unannotated Regions” (LURs) and contain novel ORFs. The designations, orphan and LUR, were based on comparative analyses of the lengths of ORFs and unannotated regions. [0120]
A total of 1258 ORFs were identified by homology searches of the GenPept database with an additional 253 ORFs identified using the GeneMark algorithm. [0121]

Example 6

Gene Clustering

In the final step of analysis, a gene clustering protocol is used to determine related ORFs within and across genomes. Gene clustering is carried out through BLAST2 pairwise comparisons of each ORF in the PATHOSEQ database (Incyte Genomics, Palo Alto Calif.) against every other ORF in the database. If two ORFs matched each other at a P-value less than or equal to 1e-15, they were placed in the same cluster. If a third ORF matched either of the first two ORFs at a P-value of less than or equal to 1e-15, the third ORF joined the cluster. Thus, clusters were formed so that any ORF in a cluster must match at least one other ORF in the cluster at less than or equal to the threshold P-value of 1e-15. The representative ORF for a cluster is the one with the best matched annotation. [0122]

Example 7

Ordering of Contiguous Sequences

The ordering of contigs has been accomplished through three types of analyses: 1) 5′/3′ sequence pair information, 2) annotation information, and 3) BLAST2 analysis of the ends of contigs. Contig ordering based on 5′/3′ sequence pairs was done by identifying all 5′/3′ sequence pairs (5′ and 3′ sequences with the same Sequence ID) that were not in the same contig, but span a gap between two contigs with the estimated distance between them of about 1.5-3.0 kb (the insert size of the library). Annotation information was used to determine contig order in two ways, either by identifying genes spanning contig gaps or by comparison with genes at the ends of contigs in related organisms with similar gene order. [0123]
Genes spanning gaps were identified by observing the N-terminal portion of an ORF at the end of one contig and the C-terminal portion of an ORF at the end of another contig. Two partial ORFs are considered to be portions of the same ORF when they meet this criteria and annotate to the same top five GenPept database entries. Comparison of two related organisms with similar gene order is used to predict contig ordering when one organism contains continuous gene order information over a region that spans a gap in the second organism. BLAST analysis of the ends of contigs was used to identify those contigs which overlapped, but failed to join because the sequence overlap did not meet the length or quality score required by PHRAP (Green, supra). Table 2 shows the ordering of the [0124] M. catarrhalis contigs as supported by one or more of these analyses.

Example 8

Extension of Partial ORFs to Full Length

Using the DNA sequences disclosed herein, an ORF is extended using a modified XL-PCR (PE Biosystems) procedure. Oligonucleotide primers, one to initiate 5′ extension and the other to initiate 3′ extension were designed using the nucleotide sequence of the known fragment and OLIGO 4.06 software (National Biosciences). The initial primers were about 22 to 30 nucleotides in length, had a GC content of about 42%, and annealed to the target sequence at temperatures of about 55 C to about 68 C. Any fragment which would result in hairpin structures and primer-primer dimerizations was avoided. The genomic DNA library was used to extend the molecule. If more than one extension was needed, additional or nested sets of primers were designed. [0125]
High fidelity amplification was obtained by performing PCR in 96-well plates using the DNA ENGINE thermal cycler (MJ Research). The reaction mix contained 2+DNA template, 200 mol of each primer, reaction buffer containing Mg, (NH[0126] ₄)₂SO₄, and β-mercaptoethanol, Taq DNA polymerase (APB), ELONGASE enzyme (Life Technologies), and Pfu DNA polymerase (Stratagene), with the following parameters for primer pair selected from the plasmid: Step 1: 94 C, 3 min; Step 2: 94 C, 15 sec; Step 3: 60 C, 1 min; Step 4: 68 C, 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68 C, 5 min; Step 7: storage at 4 C. In the alternative, parameters for the primer pair, T7 and SK+ (Stratagene), were as follows: Step 1: 94 C, 3 min; Step 2: 94 C, 15 sec; Step 3: 57 C, 1 min; Step 4: 68 C, 2 min; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68 C, 5 min; Step 7: storage at 4 C.
The concentration of DNA in each well was determined by dispensing 100 μl PICOGREEN quantitation reagent (0.25% v/v; Molecular Probes) dissolved in 1×TE and 0.5 μl of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Costar, Acton Mass.) and allowing the DNA to bind to the reagent. The plate was scanned in a Fluoroskan II (Labsystems Oy, Helsinki, Finland) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5 μl to 10 μl aliquot of the reaction mixture was analyzed by electrophoresis on a 1% agarose mini-gel to determine which reactions were successful in producing longer sequence. [0127]
The extended sequences were desalted, concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison Wis.), and sonicated or sheared prior to religation into pUC18 vector (APB). For shotgun sequencing, the digested fragments were separated on about 0.6-0.8% agarose gels, fragments were excised as visualized under UV light, and agarose removed/digested with AGARACE enzyme (promega). Extended fragments were religated using T4 DNA ligase (NEB) into pUC18 vector (APB), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transformed into competent [0128] E. coli cells. Transformed cells were selected on antibiotic-containing media, and individual colonies were picked and cultured overnight at 37 C in 384-well plates in LB/2×carb liquid media.
The cells were lysed, and DNA was amplified using Taq DNA polymerase (APB) and Pfu DNA polymerase (Stratagene) with the following parameters: Step 1: 94 C, 3 min; Step 2: 94 C, 15 sec; Step 3: 60 C, 1 min; Step 4: 72 C, 2 min; Step 5: steps 2, 3, and 4 repeated 29 times; Step 6: 72 C, 5 min; Step 7: storage at 4 C. DNA was quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries were reamplified using the conditions described above. Samples were diluted with 20% dimethysulphoxide (1:2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECT kit (APB) or the ABI PRISM BIGDYE terminator kit (PE Biosystems). [0129]

Example 9

Labeling of Probes and Hybridization Analyses

Substrate Preparation [0130]
Nucleic acids are isolated from a biological source and applied to a substrate for standard hybridization protocols by one of the following methods. A mixture of nucleic acids, a restriction digest of genomic DNA, is fractionated by electrophoresis through an 0.7% agarose gel in 1×TAE running buffer and transferred to a nylon membrane by capillary transfer using 20× saline sodium citrate (SSC). Alternatively, the nucleic acids are individually ligated to a vector and inserted into bacterial host cells to form a library. Nucleic acids are arranged on a substrate by one of the following methods. In the first method, bacterial cells containing individual clones are robotically picked and arranged on a nylon membrane. The membrane is placed on bacterial growth medium. LB agar containing carb, and incubated at 37 C for 16 hours. Bacterial colonies are denatured, neutralized, and digested with proteinase K. Nylon membranes are exposed to UV irradiation in a STRATALINKER UV-crosslinker (Stratagene) to cross-link DNA to the membrane. [0131]
In the second method, nucleic acids are amplified from bacterial vectors by thirty cycles of PCR using primers complementary to vector sequences flanking the insert. Amplified nucleic acids are purified using SEPHACRYL-400 beads (APB). Purified nucleic acids are robotically arrayed onto a glass microscope slide (Corning Science Products, Corning N.Y.). The slide is previously coated with 0.05% aminopropyl silane (Sigma-Aldrich, St. Louis Mo.) and cured at 110 C. The arrayed glass slide (microarray) is exposed to UV irradiation in a STRATALINKER UV-crosslinker (Stratagene). [0132]
Probe Preparation [0133]
DNA probes are made from mRNA templates. Five micrograms of mRNA is mixed with 1 μg random primer (Life Technologies), incubated at 70 C for 10 minutes, and lyophilized. The lyophilized sample is resuspended in 50 μl of 1× first strand buffer (cDNA Synthesis systems; Life Technologies) containing a dNTP mix, [α-[0134] ³²P]dCTP, dithiothreitol, and MMLV reverse transcriptase (Stratagene), and incubated at 42 C for 1-2 hours. After incubation, the probe is diluted with 42 μl dH₂O, heated to 95 C for 3 minutes, and cooled on ice. mRNA in the probe is removed by alkaline degradation. The probe is neutralized, and degraded mRNA and unincorporated nucleotides are removed using a PROBEQUANT G-50 column (APB). Probes are labeled with fluorescent markers, Cy3-dCTP or Cy5-dCTP (APB), in place of the radionucleotide, [³²P]dCTP.
Hybridization [0135]
Hybridization is carried out at 65 C in a hybridization buffer containing 0.5 M sodium phosphate (PH 7.2), 7% SDS, and 1 mM EDTA After the substrate is incubated in hybridization buffer at 65 C for at least 2 hours, the buffer is replaced with 10 ml of fresh buffer containing the probes. After incubation at 65 C for 18 hours, the hybridization buffer is removed, and the substrate is washed sequentially under increasingly stringent conditions, up to 40 mM sodium phosphate, 1% SDS, 1 mM EDTA at 65 C. To detect sighal produced by a radiolabeled probe hybridized on a membrane, the substrate is exposed to a PHOSPHORIMAGER cassette (APB), and the image is analyzed using IMAGEQUANT data analysis software (APB). To detect signals produced by a fluorescent probe hybridized on a microarray, the substrate is examined by confocal laser microscopy, and images are collected and analyzed using GEMTOOLS gene expression analysis software (Incyte Genomics). [0136]

Example 10

Complementary Nucleic Acid Molecules

Molecules complementary to the nucleic acid molecule, or a fragment thereof, are used to detect, decrease, or inhibit gene expression. Although use of oligonucleotides comprising from about 15 to about 30 base pairs is described, the same procedure is used with larger or smaller fragments or derivatives such as peptide nucleic acids (PNAs). Oligonucleotides are designed using OLIGO 4.06 software (National Biosciences) and a nucleic acid molecule of the Sequence Listing or fragment thereof. To inhibit transcription by preventing promoter binding, a complementary oligonucleotide is designed to bind to sequence 5′ of the ORF, most preferably about 10 nucleotides before the initiation codon of the ORF. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to the mRNA encoding the [0137] M. catarrhalis protein.

Example 11

Expression of an M. catarrhalis Protein

An [0138] M. catarrhalis nucleic acid molecule is subcloned into a vector containing an antibiotic resistance gene and the inducible T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element. Recombinant vectors are transformed into BL21(DE3) competent cells (Stratagene). Antibiotic resistant bacteria express the bacterial protein upon induction with IPTG.
The protein is synthesized as a fusion protein with FLAG which permits affinity-based purification of the recombinant fusion protein from crude cell lysates. Kits for immunoaffinity purification using monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak, Rochester N.Y.) are commercially available. Following purification the heterogeneous moiety is proteolytically cleaved from the bacterial protein at specifically engineered sites. Purified protein is used directly in the production of antibodies or in activity assays. [0139]

Example 12

Production of M. catarrhalis Protein Specific Antibodies

An [0140] M. catarrhalis produced as described above or an oligopeptide designed and synthesized using an ABI 431 A peptide synthesizer (pE Biosystems) is used to produce an antibody. Animals are immunized with the protein or an oliopeptide-KLH complex in complete Freund's adjuvant. Immunizations are repeated at intervals thereafter in incomplete Freund's adjuvant. After a minimum of seven weeks for mouse or twelve weeks for rabbit, antisera are drawn and tested for antipeptide activity. Testing involves binding the peptide to plastic, blocking with 1% bovine serum albumin, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG. Methods and machinery well known in the art are used to determine antibody titer and the amount of complex formation.

Example 13

Screening or Purifying Molecules Using Specific Binding

The nucleic acid molecule, or fragments thereof, or the protein, or portions thereof, are labeled with [0141] ³²P-dCTP, Cy3-dCTP, Cy5-dCTP (APB), or BIODIPY or FITC (Molecular Probes), respectively. Libraries of candidate molecules previously arranged on a substrate are incubated in the presence of labeled nucleic acid molecule or protein. After incubation under conditions for either a nucleic acid or amino acid sequence, the substrate is washed, and any position on the substrate retaining label, which indicates specific binding or complex formation, is assayed, and the binding molecule is identified. Data obtained using different concentrations of the nucleic acid or protein are used to calculate affinity between the labeled nucleic acid or protein and the bound molecule.

Example 14

Identification of M. catarrhalis Genes Induced During Infection

In vivo expression technology (IVET) is used with the sequences, or ORFs, to identify [0142] M. catarrhalis genes specifically induced during infection or under pathogenic conditions (Mahan et al. (1993) Science 259:686). A library of random genomic fragments of M. catarrhalis is made and ligated to a gene for a selectable marker required for survival in the host animal. Only those M. catarrhalis cells harboring a fusion sequence containing an active promoter will survive passage through the host. Fusion bearing promoters with constitutive activity are identified and discarded by examining reporter activity on laboratory medium passaged M. catarrhalis bacteria. By harvesting M. catarrhalis cells from infection sites in the host and subtraction of the identified constitutively activated genes, a list of genes turned on during infection or under pathogenic conditions are compiled.
Host induced [0143] M. catarrhalis genes are identified using the M. catarrhalis sequences and ORFs disclosed herein and the method of differential fluorescence induction described by Valdivia and Falkow, (1996; Mol Microbiol 22:367).

Example 15

Identification of M. catarrhalis Genes Required for Survival in Host

Using the [0144] M. catarrhalis genomic sequences and ORFs, genes required for survival in a host is determined using the signature-tagged transposon method described by Hensel et al. (1995; Science 269:400). A library of M. catarrhalis mutants is marked with a unique oligonucleotide sequence for each disrupted gene. After passage of the library though an infected animal or other selective environment, putative survival genes are identified by absence of the mutant from the passaged library.

Various modifications of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described as specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the above-described modes for carrying out the invention which are obvious to those skilled in the field of molecular biology or related fields are intended to be within the scope of the following claims.

TABLE 1


Contig	Size	Start	End	Locus ID	Identifier	P-value	Description

1	429	4	264	MCA101123	g2634865	5.00E−18	methylenetetrahydrofolate
							dehydrogenase
5	4258	4030	4257	MCA100094	g145409	4.00E−17	bacterioferritin
5	4258	1264	2612	MCA100203	g3402236	e−127	L-serine dehydratase
5	4258	3523	3978	MCA100205	g1673579	2.00E−51	bacterioferritin
5	4258	2	343	MCA101132	g1001512	3.00E−24	methylenetetrahydrofolate
							dehydrogenase
6	5009	41	1448	MCA100317	g1519052	e−134	succinyl CoA: 3-oxoacid
							CoA transferase
							precursor
6	5009	1777	4587	MCA100318	g1574147	0	transferrin-binding
							protein, putative
6	5009	4729	5007	MCA101039	g1786625	6.00E−13	putative
							oxidoreductase
7	6703	2960	3466	MCA100395	g3861150	6.00E−23	probable 50S ribosomal
							protein L25 (rply)
7	6703	965	2437	MCA100550	g2465556	e−155	OpuE
7	6703	3687	4250	MCA100554	g1573366	6.00E−44	peptidyl-tRNA
							hydrolase (pth)
7	6703	4491	5846	MCA100555	g1220106	e−120	hemN
7	6703	351	563	MCA101455	g2731760	1.00E−13	30S subunit ribosomal
							protein S21
8	7424	2423	3103	MCA100638	g286176	4.00E−33	negative regulator of
							pyocin genes
8	7424	5081	6058	MCA101449	g48773	3.00E−97	methyltransferase
8	7424	3218	4327	MCA101610
8	7424	4320	5060	MCA101612
8	7424	6504	6665	MCA101982
8	7424	6662	6928	MCA101983
8	7424	6925	7320	MCA101984	g1742219	1.00E−08	Exodeoxyribonuclease
							VIII (EC 3.1.11.—)
							(Exo VIII).
9	10709	465	1976	MCA100745	g347071	e−141	4-hydroxybutyrate
							coenzyme A transferase
9	10709	2306	3046	MCA100746	g3063885	5.00E−30	putative acyl-coA
							dehydrogenase
9	10709	4192	5478	MCA100748	g1923241	4.00E−69	site-specific
							recombinase
9	10709	5983	7809	MCA100749	g216913	0	principal sigma
							factor, rpoDA
9	10709	8288	8701	MCA100750
9	10709	8698	9393	MCA100751	g1574756	3.00E−12	conserved hypothetical
							transmembrane protein
9	10709	3	200	MCA101334	g154276	3.00E−22	peptide chain release
							factor 2
9	10709	9866	10330	MCA101713	g3025510	2.00E−33	putative
							transglycosylase
10	19988	12800	12973	MCA100043	g2281030	1.00E−22	ZfiA protein
10	19988	13066	13413	MCA100044
10	19988	966	2060	MCA100336	g4062697	e−121	Hypothetical protein
							in purB 5′region (orf-
							15)
10	19988	2141	3409	MCA100338	g2633742	4.00E−18	similar to
							hypothetical proteins
							from B. subtilis
10	19988	15744	16295	MCA100456	g1805560	3.00E−36	phosphoribosylglycinamide
							formyltransferase
							(EC 2.1.2.2)
10	19988	16331	17356	MCA100457	g1788845	e−130	phosphoribosylaminoimi
							dazole synthetase = AIR
							synthetase
10	19988	17685	18677	MCA100458	g3861171	2.00E−27	putative permease
							homolog (perM)
10	19988	18921	19685	MCA100459	g3212215	2.00E−11	conserved hypothetical
							protein
10	19988	5532	8192	MCA100516	g1800083	0	Alanyl-tRNA Synthetase
							(EC 6.1.1.7)
10	19988	8821	10335	MCA100518	g2632668	3.00E−69	similar to di-
							tripeptide ABC
							transporter
10	19988	3517	4892	MCA100711	g1573637	e−171	adenylosuccinate lyase
							(purB)
10	19988	11303	12571	MCA100888	g2983613	e−106	aspartokinase
10	19988	13673	13906	MCA101216	g1573976	4.00E−31	ribosomal protein L28
							(rpL28)
10	19988	13949	14101	MCA101228	g1790067	7.00E−18	50S ribosomal subunit
							protein L33
10	19988	14201	14950	MCA101234	g3342798	1.00E−29	glutamine
							cyclotransferase
							precursor
10	19988	8330	8503	MCA101481
10	19988	334	801	MCA101636	g1789103	9.00E−38	orf, hypothetical
							protein
11	14335	4618	5967	MCA100986	g1572963	e−155	conserved hypothetical
							protein
11	14335	7881	8108	MCA100989
11	14335	8089	8514	MCA100990
11	14335	8504	9154	MCA100991	g455332	2.00E−07	pilus expression
							protein
11	14335	9281	10588	MCA100992	g459551	1.00E−73	fimbrial assembly
							protein
11	14335	10856	11347	MCA100993	g1573166	3.00E−44	shikimic acid kinase I
							(aroK)
11	14335	11422	12447	MCA100994	g2661441	6.00E−88	3-dehydroquinate
							synthetase
11	14335	12538	13482	MCA100995
11	14335	13503	14108	MCA100996	g2950411	5.00E−26	hypothetical protein
							Rv3588c
11	14335	1110	2087	MCA101460	g4235484	e−142	malate dehydrogenase
11	14335	2383	3599	MCA101547	g1790853	2.00E−25	soluble lytic murein
							transglycosylase
11	14335	7292	7798	MCA101551	g455330	4.00E−15	membrane protein
11	14335	14167	14335	MCA101992
12	21410	15	647	MCA100476	g2462048	9.00E−50	monofunctional
							peptidoglycan
							transglycosylase
12	21410	993	3011	MCA100477	g2462047	0	polyphosphate kinase
12	21410	3051	3521	MCA100478	g1573243	1.00E−34	conserved hypothetical
							protein
12	21410	3641	4690	MCA100479	g1573154	e−142	chorismate synthase
							(aroC)
12	21410	5549	6016	MCA100481	g1786848	6.00E−38	protein of lipoate
							biosynthesis
12	21410	6421	7621	MCA100938	g1787162	9.00E−88	nicotinate
							phosphoribosyltransferase
12	21410	8297	9625	MCA100940	g1573601	e−123	conserved hypothetical
							protein
12	21410	9759	10676	MCA100941	g149244	3.00E−59	Lys R member
12	21410	10956	12413	MCA100942	g4456996	5.00E−90	permease for AmpC
							beta-lactamase
							expression AmpG
12	21410	12579	13343	MCA100943	g1651602	3.00E−41	Protoporphyrinogen
							oxidase (EC 1.3.3.4)
							hemK
12	21410	13406	14134	MCA100944	g1787048	1.00E−40	molybdopterin
							biosynthesis
12	21410	14383	15528	MCA100945	g3261724	2.00E−42	hypothetical protein
							Rv0647c
12	21410	17885	18445	MCA100947	g41336	9.00E−49	enterohemolysin 1
12	21410	4870	5397	MCA101603	g1573079	2.00E−71	inorganic
							pyrophosphatase (ppa)
13	31940	29883	30041	MCA100005	g3282800	2.00E−09	50S ribosomal protein
							L32
13	31940	17948	18358	MCA100019	g42833	2.00E−46	ribosomal protein L16
							(rplP) (aa 1-136)
13	31940	20208	20510	MCA100105	g1789703	3.00E−29	30S ribosomal subunit
							protein S14
13	31940	22493	22663	MCA100139	g498362	1.00E−16	ribosomal protein L30
13	31940	22675	23106	MCA100140	g1573807	8.00E−37	ribosomal protein L15
							(rpL15)
13	31940	23182	24408	MCA100141	g606234	e−111	secY
13	31940	18936	19301	MCA100153	g606244	1.00E−53	50S ribosomal subunit
							protein L14
13	31940	19325	19627	MCA100154	g1573799	3.00E−24	ribosomal protein L24
							(rpL24)
13	31940	19660	20193	MCA100155	g1573800	2.00E−71	ribosomal protein L5
							(rpL5)
13	31940	20528	20923	MCA100157	g1573802	1.00E−41	ribosomal protein S8
							(rpS8)
13	31940	21077	21607	MCA100158	g710620	7.00E−58	ribosomal protein L6
13	31940	21628	21969	MCA100159	g1573804	1.00E−32	ribosomal protein L18
							(rpL18)
13	31940	21975	22469	MCA100160	g42986	8.00E−54	S5 (rpSE) (aa 1-167)
13	31940	14176	14808	MCA100248	g1573787	4.00E−78	ribosomal protein L3
							(rpL3)
13	31940	14853	15425	MCA100249	g1037107	3.00E−70	L4
13	31940	15437	15724	MCA100250	g510688	7.00E−17	ribosomal protein L23
13	31940	15765	16586	MCA100251	g48648	e−121	ribosomal protein L2
							(AA 1-274)
13	31940	16605	16877	MCA100252	g1841326	1.00E−37	ribosomal protein S19
13	31940	16890	17216	MCA100253	g42831	1.00E−35	ribosomal protein L22
							(rplV) (aa 1-110)
13	31940	17222	17926	MCA100254	g42832	2.00E−78	ribosomal protein S3
							(rpsC) (aa 1-233)
13	31940	11780	13402	MCA100255	g48826	e−113	orfF
13	31940	10997	11554	MCA100256	g606188	1.00E−24	ORF_f217; orfE of
							ECMRED, uses 2nd start
13	31940	10381	10659	MCA100257	g2589194	1.00E−08	Glu-tRNAGln
							amidotransferase
							subunit C
13	31940	8809	10284	MCA100258	g1224069	0	amidase
13	31940	7813	8754	MCA100259	g1403365	0	BRO-2
13	31940	3925	4569	MCA100414	g3493603	5.00E−26	outer membrane protein
							homolog
13	31940	24691	25044	MCA100423	g581217	6.00E−46	ribosomal protein S13
							(aa 1-118)
13	31940	25068	25457	MCA100424	g4098575	7.00E−48	ribosomal protein S11
13	31940	25473	26111	MCA100425	g42798	4.00E−72	ribosomal protein S4
							(aa 1-206)
13	31940	26142	27107	MCA100426	g2896137	e−112	DNA-directed RNA
							polymerase alpha chain
13	31940	27162	27518	MCA100427	g2896138	3.00E−52	ribosomal large
							subunit protein L17
13	31940	29100	29645	MCA100430
13	31940	18361	18540	MCA100557	g1841330	9.00E−09	ribosomal protein L29
13	31940	7570	7746	MCA100583	g2589196	2.00E−15	Glu-tRNAGln
							amidotransferase
							subunit B
13	31940	6307	7563	MCA100584	g1224071	0	unknown
13	31940	2606	3502	MCA100588	g304968	3.00E−45	ORF_f310
13	31940	30365	31270	MCA100612	g3282803	2.00E−64	malonyl CoA-acyl
							carrier protein
							transacylase
13	31940	1	282	MCA101350	g1651578	2.00E−26	Cell division
							inhibitor MinD.
13	31940	488	748	MCA101742	g1651579	1.00E−14	Cell division
							inhibitor MinC.
13	31940	18573	18818	MCA101811	g606245	9.00E−23	30S ribosomal subunit
							protein S17
13	31940	31291	31908	MCA101812	g1173841	4.00E−62	3-ketoacyl-ACP
							reductase
13	31940	27617	28207	MCA101856	g1742075	2.00E−29	ORF_ID: o253#4; similar
							to [P45847]
13	31940	28272	28676	MCA101857	g1788666	7.00E−34	putative transporting
							ATPase
13	31940	13809	14117	MCA101858	g1573786	4.00E−45	ribosomal protein S10
							(rpS10)
13	31940	5219	5743	MCA101999	g2231996	2.00E−06	cytochrome c5
14	19619	11690	13288	MCA100149	g1001407	2.00E−80	iron utilization
							protein
14	19619	18587	19294	MCA100717	g2314220	4.00E−26	phosphatidylserine
							synthase (pssA)
14	19619	17517	18404	MCA100718	g1573417	5.00E−39	orfJ protein
14	19619	16112	16555	MCA100720	g1573816	9.00E−36	H. influenzae
							predicted coding
							region HI0787
14	19619	14601	15785	MCA100721	g4210610	e−110	DapE
14	19619	13561	14508	MCA100722	g1651916	8.00E−78	iron transport protein
14	19619	759	1838	MCA100895	g1574693	5.00E−72	UDP-N-
							acetylglucosamine
14	19619	2157	2699	MCA100896	g2632721	3.00E−18	similar to
							acetyltransferase
14	19619	2894	4285	MCA100897	g42056	e−148	(UDP-N-acetylmuramate:
							L-alanine ligase)
14	19619	4384	5265	MCA100898	g1574696	4.00E−78	D-alanine--D-alanine
							ligase (ddlB)
14	19619	5654	5914	MCA100899	g2622037	9.00E−11	unknown
14	19619	5994	6857	MCA100900	g2098748	3.00E−49	oxidative stress
							transcriptional
							regulator; OxyR
14	19619	7087	7644	MCA100901	g1064782	2.00E−63	alkyl hydroperoxide
							reductase
14	19619	8407	9966	MCA100903	g1786823	e−135	alkyl hydroperoxide
							reductase, F52a
							subunit
14	19619	10365	10556	MCA100904	g1799927	5.00E−17	similar to [P37096]
14	19619	10801	11643	MCA100905	g4514346	2.00E−67	MsmX
14	19619	6	629	MCA101403	g882476	3.00E−57	glutathione synthetase
15	28626	10223	10792	MCA100003
15	28626	27408	28103	MCA100097	g403436	3.00E−27	repressor protein
15	28626	24288	24542	MCA100178	g1001663	4.00E−16	rare lipoprotein A
15	28626	16822	17763	MCA100385	g453969	e−103	coproporphyrinogen
							oxidase
15	28626	17790	18383	MCA100386	g1573172	2.00E−52	GTP cyclohydrolase II
							(ribA)
15	28626	12359	13507	MCA100396	g1684734	2.00E−44	ORF396 protein
15	28626	10910	12217	MCA100397	g146020	2.00E−78	folypolyglutamate
							synthetase-
							dihydrofolate
							synthetase
15	28626	1297	2204	MCA100824	g1786319	7.00E−91	putative ATP-binding
							component of a
							transport system
15	28626	2319	3065	MCA100825	g1786320	9.00E−75	orf, hypothetical
							protein
15	28626	3176	3997	MCA100826	g882689	2.00E−48	ORF_o282
15	28626	6151	6777	MCA100828	g141797	6.00E−51	phosphoribosyl
							anthranilate isomerase
15	28626	6927	8117	MCA100829	g141798	e−172	tryptophan synthase
							beta-subunit
15	28626	8163	8981	MCA100830	g144288	6.00E−51	tryptophan synthase A
							protein (EC 4.2.1.20)
15	28626	766	1017	MCA100987	g2865528	2.00E−10	mono-heme c-type
							cytochrome ScyA
15	28626	9250	10096	MCA101005	g1788655	2.00E−78	acetylCoA carboxylase,
							carboxytransferase
							beta subunit
15	28626	13890	14987	MCA101042
15	28626	15277	15660	MCA101046
15	28626	15667	15975	MCA101766
15	28626	4067	5800	MCA101839	g1573733	0	prolyl-tRNA synthetase
							(proS)
15	28626	18809	20821	MCA101840	g1574278	e−166	1-deoxyxylulose-5-
							phosphate synthase (E.
							coli)
15	28626	20981	21787	MCA101843	g1573958	4.00E−56	extragenic suppressor
							(suhB)
15	28626	22787	23935	MCA101845	g1657482	2.00E−13	hypothetical protein
15	28626	28257	28442	MCA101846	g403437	2.00E−11	putative
16	22407	21035	22123	MCA100084	g1573365	e−141	conserved hypothetical
							GTP-binding protein
16	22407	3904	4449	MCA100337	g3091146	7.00E−25	iron-starvation
							protein PigA
16	22407	19532	20179	MCA100398	g3402250	4.00E−25	putative
							transcriptional
							regulator
16	22407	18427	19210	MCA100399	g1079662	1.00E−54	catabolite repression
							control protein
16	22407	16346	18019	MCA100400	g2649804	4.00E−70	L-lactate permease
							(lctP)
16	22407	152	415	MCA101103
16	22407	471	1757	MCA101104	g507736	e−167	PurA
16	22407	2286	2729	MCA101106	g2909463	2.00E−08	hypothetical protein
							Rv0274
16	22407	2747	2950	MCA101107
16	22407	2940	3770	MCA101108	g3261756	9.00E−14	hypothetical protein
							Rv0939
16	22407	4923	5546	MCA101110	g1574542	5.00E−78	endonuclease III (nth)
16	22407	5747	6997	MCA101111	g1787188	2.00E−62	putative ATP-dependent
							protease
16	22407	8306	8893	MCA101113	g581247	2.00E−32	gidB protein
16	22407	8949	9728	MCA101114	g45713	2.00E−49	unnamed protein
							product
16	22407	9744	10025	MCA101115
16	22407	10335	11093	MCA101116	g45714	4.00E−59	unnamed protein
							product
16	22407	11190	12152	MCA101117	g1573007	3.00E−49	conserved hypothetical
							protein
16	22407	12332	13051	MCA101118	g1651444	1.00E−53	3-deoxy-manno-
							octulosonate
							cytidylyltransferase
16	22407	13087	13668	MCA101119
16	22407	13707	14210	MCA101120	g972778	3.00E−23	homology to delta
							subunit of DNA
							polymerase III
16	22407	14905	16044	MCA101122	g1381737	e−170	lactate dehydrogenase
17	23210	18014	20569	MCA100120	g2772586	0	high molecular weight
							outer membrane protein
17	23210	505	1527	MCA101311	g3170587	e−105	glyceraldehyde-3-
							phosphate
							dehydrogenase homolog
17	23210	2353	3555	MCA101313	g1573894	e−102	GTP-binding protein
							(yhbZ)
17	23210	3919	4956	MCA101314	g409791	e−104	uroporphyrinogen
							decarboxylase
17	23210	6000	7055	MCA101316	g4154933	3.00E−71	Protease DO
17	23210	7823	8527	MCA101318	g1573324	1.00E−40	ABC transporter,
							permease protein
17	23210	8692	9441	MCA101319	g1431416	2.00E−12	ORF YDL244w
17	23210	9572	10231	MCA101320	g2293296	1.00E−34	putative transporter
17	23210	11483	12235	MCA101323
17	23210	13108	14196	MCA101325	g47094	e−107	3-phosphoserine
							aminotransferase (AA
							1-362)
17	23210	14309	15082	MCA101326	g1552782	5.00E−42	hypothetical protein
17	23210	15932	17658	MCA101328	g452382	e−150	2-isopropylmalate
							synthase
17	23210	7143	7448	MCA101647	g1652439	6.00E−08	hypothetical protein
17	23210	15246	15692	MCA101649	g2217944	2.00E−26	Lrp-family
							transcriptional
							regulators
17	23210	10452	10742	MCA101666	g1001663	1.00E−23	rare lipoprotein A
17	23210	20720	21990	MCA101696	g537207	7.00E−40	ORF_f277
17	23210	22380	22529	MCA101725	g996086	1.00E−09	ORFY; non-essential
							for pilus assembly
17	23210	22985	23149	MCA101847
17	23210	12265	13008	MCA101963
18	34001	23020	23238	MCA100089
18	34001	24445	24774	MCA100093
18	34001	27135	28022	MCA100416	g1890655	4.00E−90	UDP-3-O-acyl-GlcNAc
							deacetylase
18	34001	29225	29902	MCA100418
18	34001	31130	31741	MCA100421	g746400	7.00E−53	regulatory protein
18	34001	15193	15909	MCA100448	g496598	2.00E−69	ORF1
18	34001	184	930	MCA100873	g1209054	3.00E−87	EtfS
18	34001	972	1898	MCA100874	g1209055	6.00E−90	EtfL
18	34001	4318	5247	MCA100877	g309885	e−100	‘aspartate
							transcarbamoylase’
18	34001	5421	6119	MCA100878	g1786864	2.00E−43	orf, hypothetical
							protein
18	34001	6359	7432	MCA100879	g309886	3.00E−73	dihydroorotase-like
18	34001	7488	8273	MCA100880	g2113931	9.00E−18	citE
18	34001	23341	23862	MCA101248
18	34001	26268	26834	MCA101720	g433670	1.00E−70	elongation factor P
18	34001	2166	2930	MCA101753	g1653441	1.00E−20	rRNA methylase
18	34001	3046	4006	MCA101756	g901869	2.00E−78	fructose-1,6-/
							sedoheptulose-1,7-
							bisphosphate
							phosphatase
18	34001	9314	10354	MCA101758	g1788660	2.00E−42	erythronate-4-
							phosphate dehyrogenase
18	34001	10507	11499	MCA101759	g2983326	3.00E−28	hypothetical protein
18	34001	11730	12191	MCA101764	g1786586	2.00E−29	orf, hypothetical
							protein
18	34001	25125	26090	MCA101767	g1790589	7.00E−77	orf, hypothetical
							protein
18	34001	12249	13307	MCA101768	g1621601	7.00E−67	PurK
18	34001	13435	13911	MCA101769	g1574461	1.00E−53	phosphoribosylaminoimi
							dazole carboxylase
18	34001	8282	9238	MCA101775	g41552	7.00E−58	genX
18	34001	21669	22925	MCA101780
18	34001	23957	24285	MCA101781	g2649731	6.00E−23	conserved hypothetical
							protein
18	34001	31862	33821	MCA101782	g746401	0	ATP-binding protein
18	34001	30667	30945	MCA101796	g1750388	2.00E−19	orf2
18	34001	15937	16377	MCA101803	g2314656	2.00E−16	conserved hypothetical
							integral membrane
							protein
18	34001	16523	18349	MCA101806	g2896133	3.00E−24	outer membrane
							esterase
18	34001	18662	19597	MCA101808	g2294845	e−103	biotin synthase
18	34001	20305	20988	MCA101813	g3417415	1.00E−44	phosphoserine
							phosphatase
19	33778	32970	33659	MCA100015	g2459964	2.00E−36	HisX
19	33778	20378	21868	MCA100026	g608530	e−106	L-aspartate oxidase
19	33778	15834	16912	MCA100127	g968930	e−132	peptide chain release
							factor 1
19	33778	17205	18047	MCA100128	g1498753	9.00E−76	nicotinate-nucleotide
							pyrophosphorylase
19	33778	19349	20326	MCA100320	g1651337	e−116	Quinolinate synthetase
							A.
19	33778	10305	11824	MCA100473	g2313949	1.00E−98	osmoprotection protein
							(proWX)
19	33778	12732	14177	MCA100475	g1789015	e−165	succinate-semialdehyde
							dehydrogenase, NADP−
							dependent
19	33778	2058	2579	MCA100756
19	33778	4059	4889	MCA100758
19	33778	31220	32257	MCA100768	g2695825	4.00E−58	corA
19	33778	29370	31016	MCA100769	g1573928	e−119	glutathione-regulated
							potassium efflux
							system protein
19	33778	27814	29127	MCA100770	g1573294	3.00E−98	conserved hypothetical
							protein
19	33778	25151	27505	MCA100771	g2959335	0	Lon-protease
19	33778	24481	25038	MCA100772	g1754527	4.00E−16	intracellular
							septation A
19	33778	23332	23889	MCA100774	g3916254	2.00E−25	ExbB
19	33778	23892	24287	MCA100946	g3916255	1.00E−23	ExbD
19	33778	9106	9774	MCA101121	g927800	2.00E−20	Ydr533cp; CAI: 0.24
19	33778	219	1652	MCA101802
19	33778	3487	3846	MCA101805
19	33778	4651	4911	MCA101974
19	33778	6334	6705	MCA101975
19	33778	2811	3494	MCA101977
19	33778	22342	23226	MCA102006
2	1169	157	555	MCA100759	g2633670	2.00E−17	yzzE; similar to
							general stress protein
2	1169	795	1166	MCA101009	g3929904	5.00E−18	fumarate hydratase B,
							beta subunit
20	31063	848	1366	MCA100998	g396321	2.00E−57	nusG
20	31063	1476	1898	MCA100999	g2367334	7.00E−51	50S ribosomal subunit
							protein L11
20	31063	1907	2581	MCA101000	g47257	2.00E−62	L1 protein (AA 1-234)
20	31063	2920	3411	MCA101001	g1573638	9.00E−63	ribosomal protein L10
							(rpL10)
20	31063	3481	3852	MCA101002	g1573639	7.00E−25	ribosomal protein
							L7/L12 (rpL7/L12)
20	31063	4275	8360	MCA101003	g45729	0	beta-subunit of RNA
							polymerase
20	31063	8446	12564	MCA101004	g2367335	0	RNA polymerase, beta
							prime subunit
20	31063	12905	14122	MCA101239	g1573443	e−146	D-3-phosphoglycerate
							dehydrogenase (serA)
20	31063	14321	15688	MCA101240	g1573119	e−171	glutathione reductase
							(gor)
20	31063	16095	16997	MCA101241	g4062671	6.00E−73	Hypothetical protein
							HI0959
20	31063	17242	19314	MCA101242	g1574519	6.00E−81	tail specific protease
							(prc)
20	31063	20177	20935	MCA101244	g1573922	4.00E−28	conserved hypothetical
							protein
20	31063	21988	22695	MCA101246	g2314002	5.00E−13	H. pylori predicted
							coding region HP0862
20	31063	23138	23536	MCA101247	g1888564	7.00E−36	ORFX
20	31063	24093	24545	MCA101249	g4545247	6.00E−53	invasion protein
							homolog
20	31063	24726	26248	MCA101250	g2633966	5.00E−49	chromosome segregation
							SMC protein homolog
20	31063	28591	29325	MCA101251	g296030	4.00E−97	ribosomal protein S2
20	31063	29460	30314	MCA101252	g1552747	4.00E−61	elongation factor EF-
							Ts
20	31063	30482	31063	MCA101253	g1079661	2.00E−47	orotate phosphoribosyl
							transferase
20	31063	26531	28321	MCA101493	g1237015	4.00E−44	ORF4
20	31063	350	823	MCA101880
20	31063	21040	21933	MCA101950	g2983199	5.00E−07	biotin [acetyl-CoA-
							carboxylase] ligase
21	39003	30165	31499	MCA100007	g1772845	e−130	NAD (P) H-dependent
							glutamate
							dehydrogenase
21	39003	28829	29935	MCA100118	g1786552	e−134	glutathione-dependent
							formaldehyde
							dehydrogenase
21	39003	25255	26679	MCA100217	g1787999	4.00E−77	orf, hypothetical
							protein
21	39003	27082	27942	MCA100218
21	39003	27992	28813	MCA100219	g405878	1.00E−86	probable esterase
21	39003	20225	20965	MCA100226	g3220185	3.00E−31	pteridine reductase
21	39003	19027	20070	MCA100227	g882578	7.00E−55	CG Site No. 933
21	39003	21277	22656	MCA100347	g1736694	e−126	Proline transport
							protein
21	39003	24025	24876	MCA100349	g2570906	1.00E−64	stearoyl-CoA
							desaturase
21	39003	35864	38086	MCA100561	g1763284	e−163	penicillin-binding
							protein 1A
21	39003	33490	35418	MCA100562	g862902	0	high temperature
							protein G
21	39003	8041	9210	MCA101029	g1806239	1.00E−35	lipD
21	39003	16664	18907	MCA101134	g1788806	0	putative multimodular
							enzyme
21	39003	15338	16315	MCA101135	g1009431	e−106	porphobilinogen
							synthase
21	39003	13425	14354	MCA101137	g42903	e−119	ruvB gene product (AA
							1-336)
21	39003	12028	13293	MCA101138	g2909447	e−147	fadA2
21	39003	10330	11691	MCA101140	g3063883	8.00E−92	putative 3-oxoacyl-
							[acyl-carrier protein]
							reductase
21	39003	9377	10174	MCA101141	g2909445	3.00E−35	hypothetical protein
							Rv0241c
21	39003	7384	7893	MCA101143	g3046326	4.00E−55	hypoxanthine
							phosphoribosyltransferase
21	39003	4877	6769	MCA101145	g288532	0	dihydroxy acid
21	39003	2806	4254	MCA101147	g2078066	5.00E−97	betP
21	39003	1461	2414	MCA101149	g1001519	3.00E−23	hypothetical protein
21	39003	559	1209	MCA101201
21	39003	116	433	MCA101854	g2226116	2.00E−16	hypothetical protein
21	39003	38281	38810	MCA101855	g972976	3.00E−20	1-acyl-sn-glycerol-3-
							phosphate
							acyltransferase
21	39003	6901	7305	MCA101863
21	39003	14701	15213	MCA101864
22	45613	33275	34222	MCA100119	g1786405	3.00E−57	transcriptional
							regulator for nitrite
							reductase
22	45613	31023	32033	MCA100130	g1653241	1.00E−40	hemolysin
22	45613	13590	14525	MCA100133	g476229	e−150	isopropylmalate
							dehydrogenase
22	45613	40430	41209	MCA100144	g1799842	7.00E−62	sulfate/thiosulfate
							transport protein cysW
22	45613	41338	42090	MCA100171	g1799853	9.00E−60	sulfate transport
							system permease
							protein cyst.
22	45613	42522	42968	MCA100210
22	45613	42993	44153	MCA100212	g1573911	4.00E−84	ATP-dependent RNA
							helicase (rhlB)
22	45613	44209	45369	MCA100213	g1573441	2.00E−87	oxygen-independent
							coproporphyrinogen III
							oxidase
22	45613	10853	13060	MCA100223	g1000692	0	LeuA
22	45613	536	1627	MCA100312	g1790487	4.00E−49	alanine racemase 1
22	45613	1693	3003	MCA100313	g145763	e−106	DnaB replication
							protein (dnaB)
22	45613	3266	4333	MCA100314	g1786237	3.00E−66	pyridoxine
							biosynthesis
22	45613	8040	9071	MCA100353	g3758880	e−153	fructose-1,6-
							bisphosphate aldolase
22	45613	9074	9676	MCA100354	g1573280	4.00E−29	Holliday junction DNA
							helicase (ruvA)
22	45613	10292	10609	MCA100356	g1850796	6.00E−19	CynR protein
22	45613	30261	30536	MCA100450	g1573206	3.00E−17	conserved hypothetical
							protein
22	45613	28267	30132	MCA100451	g3983168	e−141	SecD
22	45613	27163	28047	MCA100452	g1573204	4.00E−55	protein-export
							membrane protein
							(secF)
22	45613	26200	26925	MCA100453	g1518782	4.00E−38	penicillin-binding
							protein 5
22	45613	39609	40322	MCA100541	g1799841	2.00E−67	sulfate/thiosulfate
							transport protein cysA
22	45613	38143	39546	MCA100542	g1881700	e−143	RadA
22	45613	36060	37833	MCA100543	g1680533	0	phospho enol pyruvate
							carboxykinase
22	45613	34862	35839	MCA100544	g2226145	4.00E−30	hypothetical protein
22	45613	15396	16193	MCA100678	g1572987	2.00E−90	exodeoxyribonuclease
							III (xthA)
22	45613	16548	18068	MCA100679	g1359473	0	lysyl-tRNA-synthase
22	45613	18097	19173	MCA100680	g1574159	e−104	DNA polymerase III,
							subunits gamma and tau
							(dnaX)
22	45613	20776	21252	MCA100682	g924993	8.00E−19	transcriptional
							regulator LtrA
22	45613	21816	22710	MCA100684	g1786984	3.00E−32	putative
							transcriptional
							regulator LYSR-type
22	45613	22855	23910	MCA100685	g2108220	1.00E−88	hemolysin
22	45613	24272	25591	MCA100686	g2209268	3.00E−69	Na+/H+ antiporter
22	45613	5347	6123	MCA100727	g1573537	1.00E−51	diadenosine-
							tetraphosphatase
							(apaH)
22	45613	4478	5278	MCA100787	g1786236	7.00E−62	S-adenosylmethionine-
							6-N′,N′-adenosyl
							dimethyltransferase
22	45613	6267	7456	MCA101090	g41422	e−121	phosphoglycerate
							kinase (AA 1-387)
22	45613	32181	32786	MCA101784
23	33140	647	814	MCA100041
23	33140	2719	3444	MCA100603	g2330641	1.00E−22	htrB
23	33140	3463	5241	MCA100604	g1788173	0	aspartate tRNA
							synthetase
23	33140	5822	7239	MCA100606	g4062776	5.00E−83	ORF_ID: o245#1
23	33140	7701	8581	MCA100608	g1574534	1.00E−72	protease, putative
							(sohB)
23	33140	8907	9644	MCA100609	g1524217	3.00E−47	hypothetical protein
							Rv0945
23	33140	9956	10741	MCA100610	g41424	3.00E−45	ORF4 (AA 1-197)
23	33140	31971	33044	MCA100705	g1788953	8.00E−98	3-deoxy-D-
							arabinoheptulosonate-
							7-phosphate synthase
23	33140	10882	11415	MCA101509	g1573653	8.00E−53	DNA-3-methyladenine
							glycosidase I (tagI)
23	33140	11492	12220	MCA101510	g3046322	2.00E−69	O-acetylserine
							synthase; CysE2
23	33140	12686	13213	MCA101511	g3046324	1.00E−24	unknown
23	33140	13720	16956	MCA101513	g940886	0	DNA polymerase III
							holoenzyme alpha
							subunit
23	33140	17151	18281	MCA101514	g1573367	3.00E−93	conserved hypothetical
							protein
23	33140	18669	19625	MCA101515	g1799725	2.00E−69	similar to [SwissProt
							Accession Number
							P39199]
23	33140	19870	20970	MCA101516	g1162959	e−123	homologous to HI0365
							in Haemophilus
							influenzae; ORF1
23	33140	21062	21676	MCA101517
23	33140	21735	22844	MCA101518	g1531668	e−122	AarC
23	33140	22996	23775	MCA101519	g4155368	3.00E−53	putative
23	33140	23844	25085	MCA101520	g1573338	e−117	histidyl-tRNA
							synthetase (hisS)
23	33140	25203	26036	MCA101521	g1573339	1.00E−12	conserved hypothetical
							protein
23	33140	26145	27266	MCA101522	g1805571	8.00E−33	serine/threonine
							protein kinase (EC
							2.7.1.—)
23	33140	27407	28831	MCA101523	g1788858	e−153	putative GTP-binding
							factor
23	33140	28941	29570	MCA101524	g2633978	1.00E−30	ribonuclease H
23	33140	29683	30894	MCA101525	g1694783	2.00E−67	1pxB
23	33140	31117	31638	MCA101526	g1787602	4.00E−11	orf, hypothetical
							protein
23	33140	136	480	MCA101883
23	33140	882	1604	MCA101889
24	33248	31423	31823	MCA101434	g1046241	8.00E−16	orf14
24	33248	25628	29158	MCA101438	g1651549	0	Transcription-repair
							coupling protein mfd
24	33248	24151	25353	MCA101439	g1685080	5.00E−30	TolB
24	33248	22836	23243	MCA101441	g1103861	1.00E−17	TolR
24	33248	22115	22702	MCA101442	g1103860	1.00E−37	TolQ
24	33248	17684	21622	MCA101443	g1574628	0	ATP-dependent helicase
							(hrpa)
24	33248	15920	16918	MCA101445	g2314661	2.00E−13	lipase-like protein
24	33248	14698	15579	MCA101446	g1840154	9.00E−36	36 kDa protein
24	33248	13519	14589	MCA101447	g4155989	1.00E−12	putative
24	33248	12383	13468	MCA101448	g2314658	7.00E−25	conserved hypothetical
							integral membrane
							protein
24	33248	11331	11747	MCA101450	g1787709	2.00E−32	orf, hypothetical
							protein
24	33248	10560	11324	MCA101451	g3192702	6.00E−28	gp19
24	33248	32602	33087	MCA101505	g1790034	3.00E−36	orf, hypothetical
							protein
24	33248	9940	10167	MCA101507	g1628368	1.00E−08	gepA
24	33248	5471	6674	MCA101512	g437700	5.00E−39	traN
24	33248	99	350	MCA102008
24	33248	1019	1525	MCA102009
24	33248	1526	2998	MCA102010
24	33248	2998	4413	MCA102011
24	33248	7022	8038	MCA102014	g2764860	9.00E−16	gene 13
24	33248	8049	8252	MCA102016
24	33248	8313	8672	MCA102017
24	33248	23253	24080	MCA102018
24	33248	8674	9030	MCA102026
24	33248	9030	9377	MCA102028
24	33248	31013	31210	MCA102029
24	33248	32232	32447	MCA102030
25	31147	830	1147	MCA100008	g3776111	6.00E−32	thioredoxin
25	31147	3	593	MCA100009	g454841	3.00E−79
25	31147	29786	30031	MCA100048	g1518927	1.00E−32	ferredoxin
25	31147	29298	29753	MCA100049	g1518926	2.00E−45	protein for
							lipopolysaccharide
							core synthesis
25	31147	12271	13725	MCA100080	g4200042	2.00E−81	exopolyphosphatase
25	31147	4751	5011	MCA100380	g663269	2.00E−13	BolA
25	31147	2616	4289	MCA100381	g2626753	2.00E−58	sulfate transporter
25	31147	1432	2072	MCA100384	g1786244	1.00E−36	orf, hypothetical
							protein
25	31147	6397	7359	MCA100487	g1052826	8.00E−97	phosphate binding
							protein
25	31147	7554	8459	MCA100488	g1574215	1.00E−70	phosphate ABC
							transporter, permease
							protein (pstC)
25	31147	8539	9348	MCA100489	g42397	9.00E−76	phoT (pstA) gene
							product (aa 1-296)
25	31147	9516	10262	MCA100490	g1790162	7.00E−94	ABC transporter, high-
							affinity phosphate-
							specific
25	31147	10496	11182	MCA100491	g1786599	6.00E−64	positive response
							regulator for pho
							regulon
25	31147	11382	12201	MCA100492	g3282775	6.00E−53	histidine protein
							kinase PhoR
25	31147	5110	5892	MCA100803	g1653285	6.00E−19	hypothetical protein
25	31147	14590	15696	MCA101453
25	31147	16710	17657	MCA101456	g2766195	3.00E−15	putative permease BhiE
25	31147	17742	18020	MCA101457	g2415545	2.00E−19	permease protein
25	31147	18338	19156	MCA101458	g1574806	7.00E−65	spermidine/putrescine
							ABC transporter
25	31147	19449	20102	MCA101459	g4539576	4.00E−10	putative morphological
							differentiation-
							associated protein
25	31147	20696	21667	MCA101461	g1881313	8.00E−80	similar to alkanal
							monooxygenase alpha
							chain
25	31147	21810	22436	MCA101462	g1788844	6.00E−70	uracil
							phosphoribosyltransferase
25	31147	23978	25966	MCA101464	g1574651	0	DNA ligase (lig)
25	31147	25990	26874	MCA101465
25	31147	27604	28056	MCA101467	g1788973	5.00E−48	small protein B
25	31147	28358	29119	MCA101468	g478986	1.00E−47	NADPH-flavin
							oxidoreductase
25	31147	15766	16581	MCA101993	g1360216	1.00E−06	ORF YLL031c
26	34279	24575	24982	MCA100071	g1787709	2.00E−33	orf, hypothetical
							protein
26	34279	23822	24559	MCA100072	g3192702	4.00E−32	gp19
26	34279	25922	28576	MCA100506	g3192704	0	gp21
26	34279	30501	30830	MCA100508
26	34279	30	378	MCA100640	g1574256	2.00E−24	H. influenzae
							predicted coding
							region HI1422
26	34279	775	1820	MCA100642	g15152	4.00E−31	alpha gene (pot.P4-
							specific DNA primase)
							(AA 1-777)
26	34279	3747	4175	MCA100645
26	34279	4724	5230	MCA100647
26	34279	5715	7454	MCA100648	g3703076	5.00E−08	putative terminase
							large subunit
26	34279	25324	25890	MCA100871	g3192703	6.00E−26	gp20
26	34279	7772	8620	MCA101290	g1574365	5.00E−78	H. influenzae
							predicted coding
							region HI1523
26	34279	8726	8929	MCA101291
26	34279	8996	9613	HCA101292
26	34279	11030	11218	MCA101295
26	34279	11362	12360	MCA101296	g4126611	2.00E−21	ORF25
26	34279	12828	13169	MCA101297
26	34279	13153	13626	MCA101299
26	34279	13623	13979	MCA101300
26	34279	14007	14438	MCA101301
26	34279	14521	14868	MCA101302
26	34279	14943	15191	MCA101303
26	34279	15247	15624	MCA101304
26	34279	15733	19257	MCA101305	g2392838	2.00E−07	unknown
26	34279	19350	19622	MCA101306	g2232363	2.00E−09	lambda phage M tail
							component homolog
26	34279	22634	23014	MCA101309
26	34279	23069	23783	MCA101409	g3192701	1.00E−44	gp18
26	34279	4281	4589	MCA101760
26	34279	5384	5770	MCA101762
26	34279	30917	31486	MCA101785
26	34279	12525	12812	MCA101793
26	34279	10141	10902	MCA101809	g3172264	4.00E−12	major head subunit;
							gp17
26	34279	21575	22135	MCA101932
26	34279	22098	22577	MCA101933
26	34279	7432	7626	MCA101935
26	34279	5227	5397	MCA102035
27	48328	3898	4593	MCA100056
27	48328	23080	24003	MCA100073	g3482882	2.00E−81	unknown
27	48328	1179	1733	MCA100106
27	48328	1882	2790	MCA100107
27	48328	43439	45661	MCA100173	g1786239	3.00E−52	organic solvent
							tolerance
27	48328	18470	18898	MCA100206	g2314029	3.00E−33	conserved hypothetical
							protein
27	48328	18957	19259	MCA100207	g3228385	1.00E−10	DsrC
27	48328	19608	19982	MCA100208	g606279	7.00E−14	ORF_f128
27	48328	20280	22904	MCA100209	g1789433	e−171	adenylylating enzyme
							for glutamine
							synthetase
27	48328	39728	40198	MCA100292	g41611	3.00E−53	GreA protein
27	48328	40220	40582	MCA100293
27	48328	40907	41812	MCA100294	g440377	8.00E−14	297 amino acids
							peptide, unknown
							function
27	48328	41954	43224	MCA100295	g1786238	1.00E−28	survival protein
27	48328	13080	13841	MCA100296	g3192702	4.00E−33	gp19
27	48328	13845	14246	MCA100297	g1046241	5.00E−30	orf14
27	48328	15183	16646	MCA100300	g3192704	e−126	gp21
27	48328	9361	10777	MCA100325	g3192699	8.00E−13	gp16
27	48328	17057	18226	MCA100681	g3294478	6.00E−74	putative integrase
27	48328	5343	5990	MCA100784	g15640	5.00E−36	antirepressor protein
							gene (aa 1-300)
27	48328	7640	9283	MCA100788	g2764873	9.00E−27	gene 18.1
27	48328	10904	11236	MCA100790
27	48328	11341	11730	MCA100791
27	48328	11814	12479	MCA100792	g3192701	4.00E−32	gp18
27	48328	24782	25846	MCA101267	g2105065	8.00E−71	hypothetical protein
							Rv3629c
27	48328	25926	26549	MCA101268	g3406829	5.00E−40	glutathione-s-
							transferase homolog
27	48328	26714	28057	MCA101269	g1789768	2.00E−93	uroporphyrinogen III
							methylase; sirohaeme
							biosynthesis
27	48328	28527	30197	MCA101270	g2565334	e−175	sulfite reductase
27	48328	30403	31599	MCA101271	g1799660	e−141	aspartate
							aminotransferase (EC
							2.6.1.1)
27	48328	32136	32504	MCA101273	g1788077	1.00E−27	orf, hypothetical
							protein
27	48328	32871	34085	MCA101274	g451651	e−139	carbamoyl phosphate
							synthetase light
							subunit
27	48328	34231	35126	MCA101275	g1781074	2.00E−41	mrr
27	48328	35218	35517	MCA101276
27	48328	35648	36154	MCA101277	g1573288	3.00E−39	conserved hypothetical
							protein
27	48328	36212	39451	MCA101278	g1750387	0	carbamoylphosphate
							synthetase large
							subunit
27	48328	1690	1878	MCA101315
27	48328	46479	47453	MCA101401	g4545243	3.00E−43	unknown
27	48328	14561	15130	MCA101644	g3192703	1.00E−17	gp20
27	48328	47519	48194	MCA101706	g4545244	4.00E−34	unknown
27	48328	6600	6881	MCA101849
27	48328	3071	3532	MCA101900
27	48328	3625	3816	MCA101901
27	48328	2	349	MCA101902
28	49617	33195	34376	MCA100162	g1573560	e−173	elongation factor Tu
							(tufA)
28	49617	34523	35461	MCA100163	g1787114	e−103	thioredoxin reductase
28	49617	29820	30191	MCA100230	g148985	3.00E−59	StrA
28	49617	30315	30785	MCA100231	g1573568	6.00E−60	ribosomal protein S7
							(rpS7)
28	49617	30948	33044	MCA100232	g41517	0	elongation factor G
28	49617	762	1895	MCA100242	g164759	9.00E−17	alanine: glyoxylate
							aminotransferase
28	49617	2047	3519	MCA100244	g1573675	e−137	aminoacyl-histidine
							dipeptidase (pepD)
28	49617	3619	4347	MCA100245	g746513	2.00E−23	D1022.4
28	49617	35607	36643	MCA100342	g3172117	5.00E−84	acyl-CoA dehydrogenase
28	49617	36644	37420	MCA100343	g2909448	3.00E−31	fadE5
28	49617	37843	38634	MCA100344	g1785900	6.00E−30	shikimate
							dehydrogenase
28	49617	38747	39349	MCA100345
28	49617	39350	40180	MCA100346	g1651539	4.00E−07	4-amino-4-
							deoxychorismate lyase.
28	49617	14395	17115	MCA100440	g3414697	0	lactoferrin binding
							protein B; LbpB
28	49617	22514	23227	MCA100449	g3414695	e−135	unknown
28	49617	40373	41422	MCA100670	g1573431	3.00E−63	conserved hypothetical
							protein
28	49617	41438	42034	MCA100671	g3328593	2.00E−29	Thymidylate Kinase
28	49617	42254	43129	MCA100672	g1573221	4.00E−76	dihydrodipicolinate
							synthetase (dapA)
28	49617	43531	44238	MCA100673	g1788820	1.00E−80	phosphoribosylaminoimi
							dazolesuccinocarboxamide
							de synthetase
28	49617	44287	44583	MCA100674	g1261932	2.00E−22	hypothetical protein
							Rv2230c
28	49617	44964	46457	MCA100675	g38754	e−161	anthranilate synthase
28	49617	47871	48461	MCA100677	g1420585	9.00E−23	ORF YOR259c
28	49617	4561	4887	MCA100806	g4062758	6.00E−28	Hypothetical protein
							HI1355
28	49617	5171	5995	MCA100807	g1778577	5.00E−38	similar to H.
							influenzae
28	49617	7002	7334	MCA100810	g536952	1.00E−32	phnA gene product
28	49617	7401	8669	MCA100811	g557262	e−141	glutamate 1-
							semialdehyde 2,1-
							aminomutase
28	49617	8987	11776	MCA100812	g1786287	0	preprotein
							translocase; secretion
							protein
28	49617	11952	12248	MCA100813
28	49617	12453	13913	MCA100961	g4033729	2.00E−92	apolipoprotein N-
							acyltransferase
28	49617	17302	20301	MCA101127	g3414688	0	lactoferrin binding
							protein A; LbpA
28	49617	22158	22340	MCA101129
28	49617	23390	24286	MCA101130	g3861035	4.00E−53	unknown
28	49617	24341	25198	MCA101131	g154231	2.00E−57	p-aminobenzoate
							synthase component I
28	49617	25891	27114	MCA101133	g2384564	e−115	beta-ketoacyl-ACP
							synthase I
28	49617	43166	43477	MCA101765
28	49617	27638	28825	MCA101786	g3924824	3.00E−18	cDNA ESTs D37429,
							D34381, yk370a12.5,
							and yk370a12.3
28	49617	20306	21928	MCA101788	g3414689	0	unknown
28	49617	6260	6820	MCA101859	g887848	3.00E−16	ORF_o326
28	49617	237	524	MCA101905
29	66986	35441	38304	MCA100016	g154417	0	DNA repair enzyme
29	66986	59667	60365	MCA100045	g1770057	3.00E−25	glutamate racemase
29	66986	26527	27261	MCA100088	g551827	1.00E−50	phosphatidylserine
							decarboxylase
29	66986	62551	62976	MCA100100	g2621609	3.00E−35	peptide methionine
							sulfoxide reductase
29	66986	32810	33283	MCA100164	g1871177	1.00E−32	unknown protein
29	66986	32188	32637	MCA100165	g1790320	4.00E−29	orf, hypothetical
							protein
29	66986	31513	32049	MCA100166	g1574395	2.00E−41	dethiobiotin synthase
							(bioD-2)
29	66986	30641	31438	MCA100167	g1574396	2.00E−26	biotin synthesis
							protein, putative
29	66986	3760	4908	MCA100170	g150277	e−144	major anaerobically
							induced outer membrane
							protein
29	66986	7578	8528	MCA100196	g1788007	e−108	phenylalanine tRNA
							synthetase, alpha-
							subunit
29	66986	8587	10980	MCA100197	g1788006	0	phenylalanine tRNA
							synthetase, beta-
							subunit
29	66986	376	2616	MCA100310	g2584871	0	nitric oxide reductase
29	66986	63073	63813	MCA100362	g1573289	6.00E−48	conserved hypothetical
							protein
29	66986	63968	64921	MCA100363	g1736517	2.00E−86	ORF_ID: o337#12;
							similar to [P44167]
29	66986	65011	65925	MCA100364	g1788268	2.00E−60	orf, hypothetical
							protein
29	66986	27579	27932	MCA100376	g1773150	3.00E−10	hypothetical 14.8 kd
							protein
29	66986	28126	29346	MCA100377	g1574398	e−134	adenosylmethionine-8-
							amino-7-oxononanoate
							aminotransfer
29	66986	29451	30593	MCA100378	g1574397	3.00E−94	8-amino-7-oxononanoate
							synthase (bioF)
29	66986	38453	38947	MCA100569	g1573216	3.00E−41	single-stranded DNA
							binding protein (ssb)
29	66986	41258	41935	MCA100572	g1067166	3.00E−67	inner membrane protein
29	66986	6768	7145	MCA100655	g2983502	3.00E−12	hypothetical protein
29	66986	56916	58574	MCA100693	g1842057	0	electron transfer
							flavoprotein-
							ubiquinone
							oxidoreductase
29	66986	55454	56770	MCA100694	g1787461	5.00E−88	enzyme in alternate
							path of synthesis of
							5-aminolevulin
29	66986	53509	54726	MCA100696	g557259	1.00E−18	orf3
29	66986	5678	6376	MCA100697	g1806180	4.00E−13	hypothetical protein
							Rv0712
29	66986	52515	52949	MCA100698	g557258	3.00E−09	hemM
29	66986	51719	52480	MCA100699	g968927	9.00E−37	orfY gene product
29	66986	50111	51057	MCA100701	g147379	e−122	phosphoribosylpyrophosphate
							synthetase (EC
							2.7.6.1)
29	66986	49534	50058	MCA100957	g4062631	1.00E−11	Cytochrome b561
29	66986	23587	25704	MCA100973	g939724	2.00E−99	putative sensor
							kinase; regulatory
							protein
29	66986	21832	22698	MCA100974	g581757	e−110	cysteine synthase
29	66986	21122	21790	MCA100975	g4155184	9.00E−19	putative
29	66986	19031	20455	MCA100977	g1789148	5.00E−69	putative enzyme
29	66986	17277	18389	MCA100979	g1573195	1.00E−82	ATP-dependent RNA
							helicase (deaD)
29	66986	14191	16212	MCA100981	g1789147	e−144	(p)ppGpp synthetase I
							(GTP
							pyrophosphokinase)
29	66986	13280	14149	MCA100982	g466773	2.00E−57	formamidopyrimidine-
							DNA glycosylase
29	66986	11637	11894	MCA100984	g1657496	1.00E−21	hypothetical protein
29	66986	61385	62110	MCA101336	g3132253	1.00E−33	ORF5
29	66986	11131	11412	MCA101783	g1435199	3.00E−26	IhfA
29	66986	49142	49360	MCA101787
29	66986	60620	60838	MCA101791
29	66986	41962	42651	MCA101800	g1174236	8.00E−30	CycJ
29	66986	47425	48129	MCA101884	g467327	9.00E−49	unknown
29	66986	33583	33888	MCA101885	g1196481	4.00E−10	unknown protein
29	66986	34239	34529	MCA101888	g1778554	3.00E−20	HI0034 homolog
29	66986	34824	35239	MCA101893	g1303791	7.00E−15	YqeJ
29	66986	2840	3361	MCA101894	g2633273	1.00E−30	similar to
							hypothetical proteins
29	66986	39252	40400	MCA101895	g1789416	7.00E−91	putative
							synthetase/amidase
29	66986	42814	43641	MCA101896	g150508	e−103	lipoprotein
29	66986	43836	44480	MCA101897	g1552774	1.00E−37	hypothetical
29	66986	44515	45558	MCA101898	g1573615	e−121	ABC transporter, ATP-
							binding protein
29	66986	45781	46777	MCA101899	g2072712	9.00E−14	mtrB
29	66986	58939	59568	MCA102050
29	66986	20802	21026	MCA102051
29	66986	12225	13193	MCA102055
30	58909	57032	58390	MCA100109	g4062412	e−165	Hypothet. 51.7 kd
							protein in dnaJ-rpsU
							interegenic region.
30	58909	44550	45806	MCA100235	g1799634	2.00E−97	NADH dehydrogenase I
							chain N (EC 1.6.5.3)
30	58909	47991	49715	MCA100331	g1574424	0	arginyl-tRNA
							synthetase (argS)
30	58909	46973	47773	MCA100332	g290446	4.00E−31	ferredoxin NADP+
							reductase
30	58909	1064	2329	MCA100463	g436156	e−127	GTPase required for
							high frequency
							lysogenization
30	58909	2502	3320	MCA100464	g606115	5.00E−55	dihydropteroate
							synthase
30	58909	3369	4094	MCA100465	g1789315	4.00E−34	orf, hypothetical
							protein
30	58909	56014	56754	MCA100615	g1183839	8.00E−73	unknown
30	58909	54292	55815	MCA100616	g148179	e−131	threonine deaminase
30	58909	53064	54086	MCA100617	g44888	e−153	NgoPII restriction and
							modification
30	58909	52624	53001	MCA100618	g606334	1.00E−30	ORF_o133
30	58909	52190	52600	MCA100619	g1147812	1.00E−23	red cell-type low
							molecular weight acid
							phosphatase
30	58909	51008	52030	MCA100620	g145431	4.00E−49	unidentified reading
							frame II
30	58909	4392	5996	MCA100757	g44839	e−139	pilB gene product (AA
							1-521)
30	58909	45970	46683	MCA100785	g1573561	5.00E−96	membrane protein
30	58909	6	854	MCA100838	g1573723	7.00E−63	heat shock protein
							(htpX)
30	58909	39210	39746	MCA101072	g1788617	2.00E−81	NADH dehydrogenase I
							chain I
30	58909	39794	40300	MCA101079	g1788616	2.00E−32	NADH dehydrogenase I
							chain J
30	58909	6340	7718	MCA101157	g2804454	e−131	C. elegans
							adenosylhomocysteinase
							(SW: P27604)
30	58909	8333	11554	MCA101159	g3523135	0	transferrin binding
							protein A; TbpA
30	58909	12590	14125	MCA101161	g3523128	0	unknown
30	58909	14403	16520	MCA101164	g3523129	0	transferrin binding
							protein B; TbpB
30	58909	17432	18442	MCA101166	g1590923	8.00E−21	conserved hypothetical
							protein
30	58909	18722	19336	MCA101167	g3861219	9.00E−47	unknown
30	58909	19375	20268	MCA101168	g1651962	3.00E−80	hypothetical protein
30	58909	22343	23683	MCA101170	g1574303	e−128	mrsA protein (mrsA)
30	58909	23858	24490	MCA101194	g1653389	9.00E−50	pyridoxamine 5-
							phosphate oxidase
30	58909	24814	25410	MCA101195	g4063381	3.00E−27	periplasmic chaperone
							protein
30	58909	25438	25635	MCA101196	g1573260	3.00E−08	mercuric ion scavenger
							protein (merP)
30	58909	25824	26192	MCA101197	g3273735	2.00E−32	NADH dehydrogenase
							chain A
30	58909	26785	27447	MCA101199	g1788624	6.00E−87	NADH dehydrogenase I
							chain B
30	58909	27619	29301	MCA101200	g1788622	0	NADH dehydrogenase I
							chain C, D
30	58909	30568	31590	MCA101202	g682765	3.00E−74	mccB
30	58909	31965	32180	MCA101203	g349635	2.00E−19	NADH dehydrogenase
							subunit
30	58909	33192	33647	MCA101205	g349636	3.00E−46	NADH dehydrogenase
							subunit
30	58909	33770	35029	MCA101206	g1799645	e−152	NADH dehydrogenase I
							chain F (EC 1.6.5.3)
30	58909	35070	38009	MCA101207	g409013	0	NADH dehydrogenase
							subunit
30	58909	38202	39188	MCA101208	g1788618	e−123	NADH dehydrogenase I
							chain H
30	58909	40440	40736	MCA101211	g1799639	4.00E−22	NADH dehydrogenase I
							chain K (EC 1.6.5.3)
30	58909	40746	42596	MCA101212	g1788614	0	NADH dehydrogenase I
							chain L
30	58909	42622	44157	MCA101213	g1799637	e−148	NADH dehydrogenase
							chain 4 (EC 1.6.5.3)
30	58909	32262	33029	MCA101966
31	65792	57101	58057	MCA100214	g1236631	2.00E−69	SfhB
31	65792	58173	58838	MCA100215	g2104329	5.00E−19	yfiH
31	65792	58955	59695	MCA100216	g1573058	1.00E−62	conserved hypothetical
							protein
31	65792	31449	32228	MCA100281	g4008034	3.00E−82	enoyl-(acyl-carrier
							protein) reductase
31	65792	32373	33071	MCA100282	g1573553	3.00E−91	ribulose-phosphate 3-
							epimerase (dod)
31	65792	33430	33732	MCA100283
31	65792	33788	34507	MCA100284
31	65792	34613	35137	MCA100286	g2959334	8.00E−17	hypothetical protein
31	65792	44547	46088	MCA100350	g1790041	e−153	2,3-
							bisphosphoglycerate-
							indpndnt
							phosphoglycerate
							mutase
31	65792	46329	47333	MCA100351	g2983365	2.00E−42	carboxyl-terminal
							protease
31	65792	59939	62041	MCA100406	g1573258	e−178	potassium/copper-
							transporting ATPase,
							putative
31	65792	62189	62968	MCA100407
31	65792	63137	63424	MCA100408	g1787108	7.00E−14	orf, hypothetical
							protein
31	65792	63494	65749	MCA100409	g45972	0	URF 2
31	65792	342	1250	MCA100493	g1787799	6.00E−40	orf, hypothetical
							protein
31	65792	5366	7711	MCA100687	g42481	0	pyruvate, water
							dikinase
31	65792	8122	8934	MCA100688	g1001627	5.00E−16	hypothetical protein
31	65792	9194	11455	MCA100689	g4062515	e−117	Hypothetical protein
							HI0115
31	65792	12030	12881	MCA100691	g1787606	5.00E−96	orf, hypothetical
							protein
31	65792	35380	36765	MCA100702	g4155857	e−162	fumerase
31	65792	37101	40302	MCA100703	g3928723	4.00E−77	putative ABC
							transporter
31	65792	41558	41968	MCA100706	g4154631	1.00E−26	bacterioferritin
							comigratory protein
31	65792	42310	43617	MCA100707	g1573080	0	conserved hypothetical
							protein
31	65792	13827	14018	MCA100733	g1778825	7.00E−21	major cold shock
							protein CspA
31	65792	33077	33430	MCA100775
31	65792	47450	48073	MCA100793	g3142729	2.00E−62	response regulator
31	65792	48273	48530	MCA100794	g2632000	3.00E−22	RpsT protein
31	65792	48820	49518	MCA100795	g1203935	7.00E−08	coded for by C.
							elegans cDNA yk86b10.5
31	65792	49766	52474	MCA100796	g525202	0	DNA topoisomerase
							(ATP-hydrolysing)
31	65792	52499	53179	MCA100797	g557844	5.00E−19	orf, len: 234, CAI:
							0.26
31	65792	53919	55553	MCA100799	g882589	4.00E−61	CG Site No. 847;
							alternate gen name
							dnaP, parB
31	65792	55986	56600	MCA100800	g1573134	6.00E−31	lipoprotein, putative
31	65792	30651	31190	MCA100907	g2981082	1.00E−51	GTP-cyclohydrolase
31	65792	28838	30289	MCA100908	g4062623	5.00E−91	Novobiocin resistance-
							related protein Nov
31	65792	27100	28536	MCA100909	g2894397	6.00E−25	TphA protein
31	65792	26354	26986	MCA100911	g2708657	3.00E−57	ribose-5-phosphate
							isomerase
31	65792	25195	26139	MCA100912	g1787100	3.00E−43	putative surface
							protein
31	65792	23910	25004	MCA100913	g1789273	4.00E−39	orf, hypothetical
							protein
31	65792	22262	23656	MCA100914	g142309	e−179	glutamine synthetase
31	65792	53226	53429	MCA101798
31	65792	21511	21816	MCA101835
31	65792	17390	18373	MCA101836	g1653422	2.00E−06	hypothetical protein
31	65792	20955	21458	MCA101838
31	65792	1604	2059	MCA101861	g2688497	7.00E−13	carboxypeptidase,
							putative
31	65792	2444	3820	MCA101862	g1907384	e−160	soluble pyridine
							nucleotide
							transhydrogenase
31	65792	4190	4996	MCA101866	g1787995	2.00E−61	orf, hypothetical
							protein
31	65792	14240	16021	MCA101867	g1651441	e−107	MsbA protein.
31	65792	18490	19170	MCA101868	g561691	5.00E−40	LpsA
31	65792	19197	19931	MCA101873	g1573652	1.00E−55	lipopolysaccharide
							biosynthesis protein
31	65792	19998	20750	MCA101874	g1573652	4.00E−56	lipopolysaccharide
							biosynthesis protein
31	65792	13103	13522	MCA101875	g3062	4.00E−41	3-dehydroquinate
							dehydratase
32	62909	50745	52567	MCA100340	g2623969	2.00E−56	putative peptidyl-
							prolyl cis-trans
							isomerase
32	62909	49000	50580	MCA100341	g42595	0	purH gene product
32	62909	42928	48531	MCA100348	g1666683	1.00E−45	hsf gene product
32	62909	8351	8881	MCA100498	g1574570	2.00E−61	conserved hypothetical
							protein
32	62909	10103	11257	MCA100501	g1789311	e−157	methionine
							adenosyltransferase 1
32	62909	11895	12551	MCA100503	g4062689	1.00E−56	heterocyst maturation
							protein (devA) homolog
32	62909	12581	13813	MCA100504	g1787362	2.00E−62	putative kinase
32	62909	6566	7315	MCA100649	g1773205	2.00E−22	similar to H.
							influenzae HI0735
32	62909	6025	6510	MCA100650	g1786736	1.00E−52	peptidyl-prolyl cis-
							trans isomerase B
							(rotamase B)
32	62909	4072	5826	MCA100651	g1574816	e−175	glutaminyl-tRNA
							synthetase (glnS)
32	62909	2634	3977	MCA100652	g3850110	3.00E−60	rrm3-pif1 helicase
							homolog
32	62909	1016	2038	MCA100654	g39921	3.00E−75	glyceraldehyde-3-
							phosphate
							dehydrogenase (AA 1-335)
32	62909	54353	54796	MCA100831	g1573349	3.00E−38	conserved hypothetical
							protein
32	62909	54874	56076	MCA100832	g1788879	e−169	putative
							aminotransferase
32	62909	56256	56636	MCA100833	g1788878	3.00E−55	orf, hypothetical
							protein
32	62909	56752	57066	MCA100834	g1573345	2.00E−30	conserved hypothetical
							protein
32	62909	57767	59620	MCA100836	g1573342	e−135	heat shock protein
							(hscA)
32	62909	59732	60067	MCA100837	g3925514	6.00E−39	ferredoxin
32	62909	60693	62453	MCA100839	g3261657	3.00E−97	ggtB
32	62909	57114	57557	MCA100980	g1799935	4.00E−17	similar to [P36540]
32	62909	14126	14635	MCA101066
32	62909	17539	17940	MCA101071	g2114470	5.00E−46	transposase homolog A
32	62909	21605	22480	MCA101075	g1788819	2.00E−68	orf, hypothetical
							protein
32	62909	22570	23385	MCA101076	g1001366	7.00E−39	hypothetical protein
32	62909	26086	26817	MCA101080	g2367307	7.00E−95
32	62909	27509	29122	MCA101082	g2367309	5.00E−89	orf, hypothetical
							protein
32	62909	29170	29628	MCA101083	g1653085	8.00E−26	adenine
							phosphoribosyltransferase
32	62909	53480	54157	MCA101204
32	62909	31514	32173	MCA101329	g1110441	2.00E−27	hypothetical product
32	62909	32281	34587	MCA101330	g290642	2.00E−80	ATPase
32	62909	35413	37533	MCA101332	g1574581	e−127	penicillin-binding
							protein 1B (ponB)
32	62909	40898	41815	MCA101337	g2367208	1.00E−56	methylase for 50S
							ribosomal subunit
							protein L11
32	62909	41865	42068	MCA101338	g2773316	2.00E−12	small DNA binding
							protein Fis
32	62909	62692	62907	MCA101380	g2407233	5.00E−23	similar to Haemophilus
							influenzae U32796
32	62909	52735	53004	MCA101444	g535709	5.00E−26	HU protein
32	62909	19635	20612	MCA101773
32	62909	26826	27470	MCA101776
32	62909	29954	30133	MCA101904	g1788076	5.00E−10	orf, hypothetical
							protein
32	62909	30170	31093	MCA101910	g1800020	1.00E−54	similar to [P37768]
32	62909	39861	40532	MCA101911	g48895	9.00E−10	acid phosphatase
32	62909	15209	16036	MCA101913	g2649017	2.00E−16	conserved hypothetical
							protein
32	62909	16414	17027	MCA101914	g1652952	5.00E−30	transposase
32	62909	20712	21326	MCA101917	g244501	5.00E−42	esterase
							II = carboxylesterase
							{EC 3.1.1.1}
32	62909	24945	25550	MCA101919	g2407235	3.00E−81	manganese superoxide
							dismutase
32	62909	9114	9776	MCA102048	g1001410	1.00E−07	hypothetical protein
32	62909	11483	11827	MCA102049
33	63563	62405	62632	MCA101035	g2314031	5.00E−10	conserved hypothetical
							protein
33	63563	56948	58870	MCA101040	g2623258	4.00E−45	putative secreted
							protein
33	63563	21766	23691	MCA101136	g2765451	8.00E−61	nitrate/nitrite
							sensory protein
33	63563	3	827	MCA101560	g2098763	7.00E−67	ThiI
33	63563	31681	31896	MCA101587	g39312	3.00E−08	barstar (AA 1-90)
33	63563	1409	2644	MCA101680	g1684734	3.00E−41	ORF396 protein
33	63563	3749	4354	MCA101682	g1786318	2.00E−61	putative carbonic
							anhdrase (EC 4.2.1.1)
33	63563	4569	8282	MCA101683	g1911243	0	alpha-subunit of
							nitrate reductase
33	63563	8347	9879	MCA101684	g2765455	0	respiratory nitrate
							reductase beta subunit
33	63563	9907	10644	MCA101685	g2765456	1.00E−40	putative chaperone
33	63563	10719	11384	MCA101686	g2765457	2.00E−63	respiratory nitrate
							reductase gamma
							subunit
33	63563	11872	12597	MCA101688	g2765458	6.00E−39	NifM protein
33	63563	12741	13922	MCA101689	g1574287	9.00E−70	molybdopterin
							biosynthesis protein
							(moeA)
33	63563	13931	15273	MCA101690	g1574545	4.00E−46	molybdenum ABC
							transporter, permease
							protein (modB)
33	63563	15349	16047	MCA101691	g973214	2.00E−49	ModA
33	63563	16157	16573	MCA101692	g899221	1.00E−26	potential molybdenum-
							pterin-binding-protein
33	63563	16659	17036	MCA101693	g1001213	1.00E−26	molybdopterin (MPT)
							converting factor,
							subunit 2
33	63563	17122	17355	MCA101694	g1673309	1.00E−09	hypothetical protein
33	63563	17375	17827	MCA101695	g4185548	2.00E−27	molybdenum cofactor
							biosynthesis protein C
33	63563	18520	19008	MCA101697	g42009	2.00E−50	moaB
33	63563	19257	19745	MCA101698	g1790345	5.00E−20	orf, hypothetical
							protein
33	63563	19849	20817	MCA101699	g1574526	1.00E−73	molybdenum cofactor
							biosynthesis protein A
							(moaA)
33	63563	21099	21722	MCA101700	g2765450	1.00E−57	nitrate/nitrite
							regulatory protein
33	63563	24027	25301	MCA101702	g2765452	e−100	nitrate extrusion
							protein
33	63563	25322	26662	MCA101703	g2765453	e−131	nitrate extrusion
							protein
33	63563	26767	27003	MCA101704	g43593	7.00E−25	IS1016-V6
33	63563	27101	27838	MCA101705	g1256835	2.00E−37	moeB gene product
33	63563	30824	31012	MCA101707	g39312	6.00E−08	barstar (AA 1-90)
33	63563	31908	32282	MCA101708	g532528	5.00E−15	ribonuclease precursor
33	63563	44513	44764	MCA101912
33	63563	59342	60850	MCA101915	g1772622	3.00E−30	HecB
33	63563	63286	63563	MCA101916
34	89047	54807	56590	MCA100174	g2984323	4.00E−67	hypothetical protein
34	89047	72751	73173	MCA100188	g1788522	2.00E−25	possible subunit of
							heme lyase
34	89047	64432	65214	MCA100272	g1799711	8.00E−72	pseudouridylate
							synthase I (EC
							4.2.1.70)
34	89047	64078	64287	MCA100273	g142459	7.00E−25	initiation factor 1
34	89047	16260	18866	MCA100326	g1651269	0	Leucine-tRNA ligase
							(EC 6.1.1.4).
34	89047	67834	68322	MCA100327	g1573775	6.00E−27	conserved hypothetical
							protein
34	89047	68604	69926	MCA100329
34	89047	70103	72067	MCA100330	g1174237	e−175	CycK
34	89047	8218	9123	MCA100410	g1420863	e−140	oligopeptidepermease
34	89047	9349	11319	MCA100411	g1420859	0	oligopeptidepermease
34	89047	11462	11734	MCA100412	g1817528	7.00E−13	component protein of
							adhesin complex
34	89047	12117	12434	MCA100413	g1817528	1.00E−14	component protein of
							adhesin complex
34	89047	31288	32337	MCA100432	g3212213	e−120	H. influenzae
							predicted coding
							region HI1126.1
34	89047	30886	31281	MCA100623	g3212214	8.00E−48	H. influenzae
							predicted coding
							region HI1127
34	89047	3573	4214	MCA100666	g1573906	6.00E−96	H. influenzae
							predicted coding
							region HI0882
34	89047	4621	6105	MCA100667	g1420860	0	oligopeptidepermease
34	89047	6109	7032	MCA100668	g1420861	e−145	oligopeptidepermease
34	89047	7081	8115	MCA100669	g1420862	e−163	oligopeptidepermease
34	89047	26541	28064	MCA100734	g2984319	2.00E−95	Na (+): solute symporter
							(Ssf family)
34	89047	24901	25710	MCA100736	g1513082	5.00E−67	ATPase
34	89047	23328	24365	MCA100738	g1786606	8.00E−89	S-
							adenosylmethionine: tRNA
							ribosyltransferase-
							isomerase
34	89047	22063	23202	MCA100739	g1573209	e−147	tRNA-guanine
							transglycosylase (tgt)
34	89047	20280	21854	MCA100740	g536958	2.00E−74	yjdB gene product
34	89047	19010	19351	MCA100742	g1573052	7.00E−15	conserved hypothetical
							protein
34	89047	72176	72649	MCA100857	g929791	1.00E−22	periplasmic or inner
							membrane associated
							protein
34	89047	60817	61410	MCA101043	g312708	5.00E−41	miaE
34	89047	59356	60669	MCA101044	g1790609	8.00E−39	orf, hypothetical
							protein
34	89047	57906	58931	MCA101045	g1573704	7.00E−40	conserved hypothetical
							protein
34	89047	56828	57394	MCA101047	g3328430	3.00E−71	Deoxycytidine
							triphosphate deaminase
							family protein
34	89047	52985	53889	MCA101051	g2636549	2.00E−22	similar to
							hypothetical proteins
34	89047	51712	52935	MCA101052	g216628	4.00E−52	UbiH (VisB)
34	89047	50505	51353	MCA101053	g1787880	7.00E−32	putative transport
							protein
34	89047	48105	50117	MCA101054	g148182	e−177	rep helicase
34	89047	46737	47753	MCA101056	g537005	4.00E−58	ORF_f337
34	89047	74796	75440	MCA101231	g4520134	7.00E−73	adenylate kinase
34	89047	78867	80283	MCA101233	g3861163	9.00E−74	2-
							acylglycerophosphoetha
							nolamine
							acyltransferase
34	89047	82080	83144	MCA101235	g1573700	1.00E−28	conserved hypothetical
							protein
34	89047	85493	88297	MCA101238	g1573699	2.00E−69	conserved hypothetical
							protein
34	89047	45297	45752	MCA101341	g1790038	3.00E−37	protein export;
							molecular chaperone
34	89047	44704	45165	MCA101342	g41300	4.00E−46	dUTPase (dut)
34	89047	44243	44665	MCA101343	g2984288	1.00E−33	acetylglutamate kinase
34	89047	43444	44199	MCA101344	g2462049	1.00E−14	hypothetical protein
34	89047	42700	43350	MCA101345	g1763619	6.00E−19	potassium channel
							alpha subunit
34	89047	39885	40328	MCA101347	g42848	6.00E−32	ribosome protein L9
							(aa 1-149)
34	89047	39641	39865	MCA101348	g1573530	5.00E−29	ribosomal protein S18
							(rpS18)
34	89047	39224	39610	MCA101349	g42845	2.00E−35	ribosomal protein S6
							(aa 1-131)
34	89047	36447	37520	MCA101351	g1789272	1.00E−96	tetrahydrofolate-
							dependent
							aminomethyltransferase
34	89047	35751	36128	MCA101352	g1789271	8.00E−40	carrier of aminomethyl
							moiety via lipoyl
							cofactor
34	89047	32628	35462	MCA101353	g304892	0	gcvHP
34	89047	28777	30564	MCA101356	g3212231	e−141	TonB-dependent
							receptor, putative
34	89047	73261	74523	MCA101532
34	89047	45820	46071	MCA101632	g3860768	7.00E−16	glutaredoxin 3
34	89047	62090	63166	MCA101727	g1922276	2.00E−15	porin
34	89047	25927	26316	MCA101860	g4545096	5.00E−09	unknown
34	89047	38043	38363	MCA101920	g4062756	3.00E−08	Hypothetical protein
							HI1446
34	89047	66384	67498	MCA101922	g1420975	e−130	aspartate semialdehyde
							dehydrogenase
34	89047	57510	57803	MCA102061
34	89047	403	2859	MCA102062	g2983163	5.00E−07	outer membrane protein c
34	89047	3164	3520	MCA102063
34	89047	38496	38981	MCA102068
34	89047	13061	14095	MCA102070	g4456807	4.00E−07	hypothetical protein
34	89047	40804	41724	MCA102072
34	89047	41911	42456	MCA102073	g1790149	3.00E−12	orf, hypothetical
							protein
35	96109	63603	63740	MCA100010	g3603060	9.00E−11	ribosomal protein L36
35	96109	63882	64673	MCA100011	g609333	6.00E−61	orf272
35	96109	781	1275	MCA100095	g1789019	5.00E−25	orf, hypothetical
							protein
35	96109	31479	31784	MCA100151	g149064	4.00E−07	insb (putative);
							putative
35	96109	16679	17584	MCA100238	g1574277	9.00E−55	geranyltranstransferase
							(ispA)
35	96109	15484	16293	MCA100239	g146864	5.00E−60	A/G-specific adenine
							glycosylase
35	96109	14399	14971	MCA100241	g1314160	3.00E−20	mitochondrial nuclease
35	96109	330	551	MCA100571	g1173842	2.00E−20	acyl carrier protein
35	96109	91699	93600	MCA100613	g1574199	0	threonyl-tRNA
							synthetase (thrS)
35	96109	18008	18937	MCA100723	g1574400	3.00E−61	2-hydroxyacid
							dehydrogenase
35	96109	19173	22007	MCA100724	g1786245	0	probable ATP-dependent
							RNA helicase
35	96109	23729	25783	MCA100726	g2695959	0	fadH
35	96109	64879	65883	MCA100851	g2198496	2.00E−51	B1306.06c protein
35	96109	68453	68746	MCA100854	g144052	5.00E−18	outer membrane protein A
35	96109	69092	69673	MCA100855	g1573697	3.00E−46	conserved hypothetical
							protein
35	96109	69937	71532	MCA100856	g790611	9.00E−63	unknown
35	96109	72055	72594	MCA100858	g2160520	2.00E−32	ORF1; similar to E
							coli L28082
35	96109	72778	73755	MCA100859
35	96109	73860	74870	MCA100860	g3257505	2.00E−32	homocysteine S-
							methyltransferase
35	96109	89648	90142	MCA100884	g290449	6.00E−45	initiation factor 3
35	96109	86580	88901	MCA100886	g1790622	e−148	putative enzyme
35	96109	83852	85201	MCA100889	g2558473	e−124	Na-translocating NADH-
							quinone reductase
							alpha-subunit
35	96109	82641	83837	MCA100890	g1573123	e−138	NADH: ubiquinone
							oxidoreductase,
							subunit B (nqrB)
35	96109	81848	82621	MCA100891	g2558475	2.00E−42	Na-translocating NADH-
							quinone reductase
							gamma-subunit
35	96109	81207	81806	MCA100892	g1573125	2.00E−71	NADH: ubiquinone
							oxidoreductase, Na
							translocating
35	96109	80542	81147	MCA100893	g2558477	2.00E−78	Na-translocating NADH-
							quinone reductase
							subunit 5
35	96109	79287	80495	MCA100894	g1573127	e−164	Na-translocating NADH-
							quinone reductase
							beta-subunit
35	96109	22117	23637	MCA100915	g1001214	e−134	hypothetical protein
35	96109	2411	4147	MCA100916	g1786265	0	acetolactate synthase
							III, val sensitive,
							large subunit
35	96109	4168	4656	MCA100917	g1786266	6.00E−44	acetolactate synthase
							III, val sensitive,
							small subunit
35	96109	4835	5848	MCA100918	g2529237	e−125	acetohydroxy acid
							isomeroreductase
35	96109	5960	6370	MCA100919
35	96109	6718	6918	MCA100920	g4454361	4.00E−22	cold shock protein,
							CSPA
35	96109	7163	7651	MCA100921	g1573284	2.00E−42	crossover junction
							endodeoxyribonuclease
							(ruvC)
35	96109	7852	8388	MCA100922
35	96109	8484	9779	MCA100923	g3298336	1.00E−65	NorM
35	96109	10000	11088	MCA100924	g1574692	5.00E−58	cell division protein
							(ftsW)
35	96109	11357	12736	MCA100925	g1574691	1.00E−75	UDP-N-
							acetylmuramoylalanine-
							-D-glutamate ligase
35	96109	12938	13273	MCA100926	g2735324	7.00E−44	PII-protein
35	96109	66095	66631	MCA100978	g3323304	7.00E−13	glpG protein, putative
35	96109	26724	27458	MCA101006	g473823	3.00E−85	‘methionine
							aminopeptidase’
35	96109	27687	30377	MCA101007	g39257	e−153	uridylyl transferase
35	96109	30510	31373	MCA101008
35	96109	32708	33978	MCA101010	g1788783	3.00E−40	putative prophage
							integrase
35	96109	35233	36276	MCA101012
35	96109	36398	37465	MCA101013
35	96109	37547	37858	MCA101014
35	96109	37855	38175	MCA101015
35	96109	56595	57344	MCA101109	g1573676	4.00E−56	integrase/recombinase
							(xerC)
35	96109	39637	39939	MCA101486
35	96109	40057	40410	MCA101487
35	96109	45467	46231	MCA101490	g1573242	2.00E−36	ribonuclease BN (rbn)
35	96109	46598	46957	MCA101491	g3493605	3.00E−30	Trp repressor binding
							protein
35	96109	47185	47616	MCA101492
35	96109	48860	49144	MCA101494	g149688	3.00E−32	htpA
35	96109	49273	50910	MCA101495	g499206	0	GroEL
35	96109	51130	51963	MCA101496	g1789192	1.00E−74	prolipoprotein
							diacylglyceryl
							transferase
35	96109	51990	52829	MCA101497	g2258280	2.00E−97	thymidylate synthase
35	96109	52856	53290	MCA101498	g665643	1.00E−28	dihydrofolate
							reductase
35	96109	53413	54426	MCA101499	g1573128	3.00E−47	lipoprotein, putative
35	96109	54579	55025	MCA101500
35	96109	55115	56281	MCA101501	g216628	1.00E−35	UbiH (VisB)
35	96109	57647	58471	MCA101503	g1790242	4.00E−80	diaminopimelate
							epimerase
35	96109	58748	59965	MCA101504	g1929094	e−110	LysA protein
35	96109	60612	61766	MCA101506	g1405880	5.00E−83	acetate kinase
35	96109	62334	63320	MCA101508	g1574131	e−127	phosphate
							acetyltransferase
							(pta)
35	96109	26139	26477	MCA101763	g2564977	4.00E−09	hypothetical protein
35	96109	41837	43138	MCA101842	g1033120	3.00E−15	ORF_o469
35	96109	85730	86452	MCA101876	g836646	9.00E−64	phosphoribosylformimino-
							5-aminoimidazole
							carboxamide
35	96109	89243	89524	MCA101877	g42742	2.00E−11	rimI protein (AA 1-161)
35	96109	75011	75493	MCA101878	g4062570	5.00E−37	4-hydroxyphenylacetate
							3-monooxygenase (EC
							1.14.13.3)
35	96109	75733	77289	MCA101881	g1787597	7.00E−94	putative pump protein
							(transport)
35	96109	77651	79135	MCA101882	g1573949	0	catalase (hktE)
35	96109	38185	38586	MCA101930
35	96109	40762	41004	MCA102021	g2313086	1.00E−08	DNA primase (dnaG)
35	96109	43196	43354	MCA102022
35	96109	95181	95342	MCA102078
36	92407	91233	91847	MCA100081	g2635437	1.00E−27	similar to protease IV
36	92407	50092	50511	MCA100085	g1574283	3.00E−53	ribosomal protein L13
							(rpL13)
36	92407	49696	50073	MCA100086	g241867	3.00E−44	ribosomal protein S9
							homolog = rpsI
36	92407	7088	7378	MCA100136	g2865528	1.00E−13	mono-heme c-type
							cytochrome ScyA
36	92407	7748	8335	MCA100137	g516878	3.00E−35	cytochrome c4
							preprotein
36	92407	14107	15696	MCA100530	g581070	e−144	acyl coenzyme A
							synthetase
36	92407	12531	13733	MCA100531	g1573978	2.00E−83	DNA/pantothenate
							metabolism
							flavoprotein (dfp)
36	92407	11001	12140	MCA100532	g551299	e−106	Na+/H+ antiporter
36	92407	16025	17620	MCA100708	g581070	e−166	acyl coenzyme A
							synthetase
36	92407	17919	18623	MCA100709	g1079663	6.00E−79	RNase PH
36	92407	18634	19089	MCA100710
36	92407	19908	20546	MCA100712	g436881	2.00E−34	outer membrane
							phospholipase A
36	92407	20579	21427	MCA100713
36	92407	21387	21977	MCA100714
36	92407	21974	22960	MCA100715
36	92407	22957	23763	MCA100716
36	92407	816	1589	MCA100752	g2984360	7.00E−71	thiamine biosynthesis,
							thiazole moiety
36	92407	1761	3098	MCA100753	g2960158	7.00E−59	hypothetical protein
							Rv3734c
36	92407	3243	5234	MCA100754	g1574731	0	methionyl-tRNA
							synthetase (metG)
36	92407	5571	6977	MCA100755	g41206	e−132	cysteinyl-tRNA
							synthetase
36	92407	61788	63133	MCA100840	g1788963	e−156	GTP-binding export
							factor
36	92407	63356	64015	MCA100842	g1788109	4.00E−20	orf, hypothetical
							protein
36	92407	64186	64992	MCA100843	g1789437	4.00E−43	bacitracin resistance
36	92407	65314	65850	MCA100844	g3851182	5.00E−14	unknown
36	92407	65942	66205	MCA100845
36	92407	66244	67065	MCA100846	g396375	5.00E−64	4-hydroxybenzoate-
							octaprenyl transferase
36	92407	67362	68897	MCA100847	g1449339	e−137	pitB
36	92407	69294	69974	MCA100848	g606374	9.00E−53	ORF_f231
36	92407	70365	70850	MCA100849	g1574067	2.00E−34	conserved hypothetical
							protein
36	92407	70982	71563	MCA100850	g497127	2.00E−55	RNase T
36	92407	38857	39717	MCA100927	g4376782	5.00E−12	CT391 hypothetical
							protein
36	92407	40914	41549	MCA100929	g3860928	5.00E−25	ABC transporter ATP-
							binding protein
36	92407	42061	44601	MCA100931	g1573874	0	ATP-dependent Clp
							protease, ATPase
							subunit (clpB)
36	92407	45517	45870	MCA100933	g1574279	2.00E−28	stringent starvation
							protein B (sspB)
36	92407	45891	46442	MCA100934	g42998	6.00E−33	SSP (AA1-212)
36	92407	46643	47320	MCA100935	g2642363	1.00E−39	cytochrome c1
36	92407	47395	48567	MCA100936	g2642362	e−133	cytochrome b
36	92407	48597	49166	MCA100937	g2642361	4.00E−48	Fe-S protein
36	92407	88972	90090	MCA101033	g305386	6.00E−21	recombination protein
36	92407	81971	82912	MCA101037	g1377868	2.00E−47	cbb3-type cytochrome c
							oxidase CcoP subunit
36	92407	71602	72657	MCA101086	g3868712	e−114	dihydroorotase
36	92407	72855	74180	MCA101087	g1574583	0	argininosuccinate
							synthetase (argG)
36	92407	74397	74897	MCA101088
36	92407	75049	75960	MCA101089	g3643996	2.00E−30	putative regulatory
							protein
36	92407	76983	78173	MCA101091	g152210	4.00E−68	nitrogen fixation
							protein fixG
36	92407	79617	80960	MCA101093	g1552601	e−179	FixNd
36	92407	81064	81636	MCA101094	g1002879	3.00E−56	CcoO
36	92407	83103	84722	MCA101097	g1574630	0	CTP synthetase (pyrG)
36	92407	84893	85729	MCA101098	g4235471	e−114	2-dehydro-3-
							deoxyphosphooctonate
							aldolase
36	92407	85823	87097	MCA101099	g1789141	e−156	enolase
36	92407	87210	87455	MCA101100	g1789105	4.00E−08	orf, hypothetical
							protein
36	92407	87621	88316	MCA101101	g1573673	3.00E−36	conserved hypothetical
							protein
36	92407	39980	40804	MCA101148	g3860927	4.00E−24	unknown
36	92407	59021	60271	MCA101153	g42913	1.00E−58	ORF 45 peptide (AA 1-400)
36	92407	55081	58941	MCA101154	g42914	1.00E−59	SbcC (AA 1-1048)
36	92407	51152	52987	MCA101156	g581463	0	homologous to E. coli
							gidA
36	92407	35356	36111	MCA101172	g1651445	2.00E−42	SmtA protein.
36	92407	33986	35242	MCA101173	g1245347	2.00E−43	AlgI
36	92407	30688	31161	MCA101176	g2765835	2.00E−29	hypothetical protein
36	92407	29194	30474	MCA101177	g3132889	1.00E−62	WaaA
36	92407	26469	28985	MCA101178	g1574460	e−160	aminopeptidase N
							(pepN)
36	92407	25542	26057	MCA101179	g663068	1.00E−26	PAL
36	92407	8594	9688	MCA101272
36	92407	9676	10008	MCA101294
36	92407	24074	24832	MCA101848
36	92407	36281	37267	MCA101850
36	92407	37432	38508	MCA101851	g3860926	1.00E−08	unknown
36	92407	60775	61569	MCA101909	g1788964	2.00E−15	orf, hypothetical
							protein
36	92407	81687	81869	MCA101928
36	92407	53341	54315	MCA101944
36	92407	54504	54968	MCA101945
37	99629	69767	70210	MCA100038	g1718488	6.00E−34	FabZ
37	99629	70275	71039	MCA100039	g1786378	3.00E−77	UDP-N-
							acetylglucosamine
							acetyltransferase
37	99629	71432	72897	MCA100082	g1573742	e−119	sodium-dependent
							transporter, putative
37	99629	76489	78342	MCA100169	g2599340	2.00E−40	protein-disulfide
							reductase
37	99629	51376	52041	MCA100276	g2865530	3.00E−30	cytochrome c
							maturation protein B
37	99629	73294	74871	MCA100290	g142301	e−168	cytochrome d subunit
							Ia
37	99629	74913	76046	MCA100291	g1786954	2.00E−99	cytochrome d terminal
							oxidase polypeptide
							subunit II
37	99629	66172	68571	MCA100323	g1552754	e−123	hypothetical protein
37	99629	68643	69560	MCA100324	g1573936	2.00E−56	UDP-3-O-(3-
							hydroxymyristoyl)-
							glucosamine N-
							acyltransfer
37	99629	33622	34110	MCA100374	g1574669	1.00E−31	thioredoxin, putative
37	99629	32014	33450	MCA100375	g1573139	e−105	amino acid carrier
							protein, putative
37	99629	2692	5811	MCA100461	g438854	0	envD homologue; ORFB
37	99629	5884	7308	MCA100564	g3184190	3.00E−77	OprM
37	99629	8308	9618	MCA100566	g1061260	2.00E−68	putative protein
37	99629	9973	11343	MCA100567	g1788397	e−165	orf, hypothetical
							protein
37	99629	11391	12323	MCA100568	g2314272	6.00E−88	cytosine specific DNA
							methyltransferase
							(BSP6IM)
37	99629	2	532	MCA100700	g1786393	5.00E−27	orf, hypothetical
							protein
37	99629	56471	57733	MCA100776	g1651420	e−145	Serine-tRNA ligase (EC
							6.1.1.11)
37	99629	57951	59921	MCA100777	g2367177	0	transketolase 1
							isozyme
37	99629	60119	60835	MCA100778	g3417448	1.00E−67	UMP kinase
37	99629	60950	61501	MCA100779	g3417449	1.00E−63	ribosome recycling
							factor
37	99629	61598	62323	MCA100780	g1786371	5.00E−54	orf, hypothetical
							protein
37	99629	62522	63199	MCA100781	g1262332	5.00E−39	CDP-diglyceride
							synthetase
37	99629	63358	64560	MCA100782	g1786369	3.00E−85	putative ATP-binding
							component of a
							transport system
37	99629	64584	65951	MCA100783	g1552753	8.00E−83	hypothetical
37	99629	34923	35243	MCA100789	g142304	3.00E−52	ferredoxin I
37	99629	1269	2564	MCA100852	g532310	1.00E−61	42 kDa protein
37	99629	26942	30208	MCA101055	g2367096	0	isoleucine tRNA
							synthetase
37	99629	83288	84046	MCA101084	g1789140	3.00E−18	orf, hypothetical
							protein
37	99629	30484	31758	MCA101163	g4062560	e−147	Uracil transport
							protein
37	99629	38692	40539	MCA101256
37	99629	40499	41389	MCA101257
37	99629	43223	46123	MCA101259	g1574225	0	valyl-tRNA synthetase
							(valS)
37	99629	46207	47085	MCA101260	g303628	e−161	MboI methyltransferase A
37	99629	47093	47932	MCA101261	g303629	e−151	MboI endonuclease
37	99629	47937	48755	MCA101262	g303630	e−145	MboI methyltransferase C
37	99629	50795	51373	MCA101265	g46024	2.00E−25	helA
37	99629	26437	26910	MCA101360	g151348	3.00E−35	signal peptidase II
37	99629	25749	26177	MCA101361	g151349	2.00E−26	ORF149
37	99629	24426	25547	MCA101362	g1835114	1.00E−95	homoserine O-
							acetyltransferase
37	99629	23029	23605	MCA101364	g4062259	6.00E−14	Sel-1 protein
37	99629	20479	22755	MCA101365	g308942	0	major outer membrane
							protein
37	99629	18600	20063	MCA101366	g38720	0	IMP dehydrogenase
37	99629	17326	18006	MCA101368	g3135321	7.00E−33	putative
							thiol: disulfide
							interchange protein
							precursor
37	99629	15653	16846	MCA101369	g45329	8.00E−97	homoserine
							dehydrogenase
37	99629	14813	15373	MCA101370	g1790296	1.00E−55	orf, hypothetical
							protein
37	99629	13917	14735	MCA101371	g606086	6.00E−72	ORF_f286
37	99629	78730	80198	MCA101417	g141886	0	acetaldehyde
							dehydrogenase II
37	99629	80403	81914	MCA101418	g2635246	e−118	similar to
							sodium/proton-
							dependent alanine
							carrier prot
37	99629	82372	82926	MCA101419	g3322862	1.00E−33	Tp70 protein
37	99629	84049	84567	MCA101421
37	99629	98444	98752	MCA101422	g216636	3.00E−21	ribosomal protein L21
37	99629	85377	86027	MCA101423	g4102010	2.00E−38	putative transposase
37	99629	86093	86667	MCA101424	g4512224	2.00E−26	Similar to IS1301 of
							Neisseria meningitidis
37	99629	86955	88568	MCA101426	g1747491	0	alxA
37	99629	88573	89919	MCA101427	g1685099	4.00E−56	HSDS
37	99629	91158	94300	MCA101429	g1685100	0	HSDR
37	99629	94381	95240	MCA101430	g1786518	6.00E−66	putative
							oxidoreductase
37	99629	95287	95940	MCA101431	g1574733	5.00E−72	NAD(P)H-flavin
							oxidoreductase
37	99629	96051	97094	MCA101432	g1303964	2.00E−70	YqjM
37	99629	97366	98229	MCA101433	g150233	6.00E−30	nahR protein precursor
37	99629	98820	99074	MCA101440	g216637	2.00E−28	ribosomal protein L27
37	99629	13079	13333	MCA101463	g1518927	6.00E−28	ferredoxin
37	99629	13439	13879	MCA101466	g1575483	3.00E−23	LporfX
37	99629	12334	13065	MCA101598	g4155637	9.00E−79	putative
37	99629	53924	54736	MCA101923	g765096	2.00E−94	heat-shock sigma
							factor
37	99629	36268	37779	MCA101924	g1787309	e−103	putative virulence
							factor
37	99629	37994	38530	MCA101929	g4079828	8.00E−45	N-acetyl-
							anhydromuramyl-L-
							alanine amidase
37	99629	41474	42911	MCA101936	g2633081	e−119	similar to 2-
							oxoglutarate/malate
							translocator
37	99629	48799	49662	MCA101938	g580726	7.00E−63	Portion of
							hypothetical protein
37	99629	52121	52933	MCA101939	g3513356	3.00E−39	hypothetical protein
37	99629	89930	91132	MCA102002
38	94750	82819	83559	MCA100037	g1573162	3.00E−71	tRNA (guanine-N1)-
							methyltransferase
							(trmD)
38	94750	83736	84065	MCA100220	g1800011	8.00E−36	ribosomal protein L19
38	94750	84195	84599	MCA100221	g145063	8.00E−31	two-subunit pilin
							precursor
38	94750	38362	39300	MCA100287
38	94750	39368	40069	MCA100288	g39705	3.00E−27	fimC
38	94750	37413	38177	MCA100301	g1573311	4.00E−49	conserved hypothetical
							protein
38	94750	36351	37259	MCA100302	g1786208	7.00E−49	putative regulator
38	94750	43520	43906	MCA100403	g1055071	7.00E−33	C23G10.2 gene product
38	94750	40106	42352	MCA100405	g147345	e−140	primosomal protein n'
38	94750	601	1360	MCA100435	g2633826	1.00E−30	similar to
							hypothetical proteins
38	94750	1401	2000	MCA100436	g1001747	1.00E−40	alkaline phosphatase-
							like
38	94750	2433	3071	MCA100437	g1574697	4.00E−12	cell division protein
							(ftsQ)
38	94750	3143	4201	MCA100438	g2738588	5.00E−23	cell division protein
38	94750	77707	78381	MCA100467	g1079807	9.00E−42	RstA
38	94750	79179	80048	MCA100469	g1742648	4.00E−37	Sensor protein RstB
							(EC 2.7.3.—).
38	94750	81833	82078	MCA100471	g1573164	3.00E−25	ribosomal protein S16
							(rpS16)
38	94750	82288	82782	MCA100472	g1573163	7.00E−26	conserved hypothetical
							protein
38	94750	29640	30077	MCA100521	g4164224	3.00E−55	ferric uptake
							regulator
38	94750	30269	31297	MCA100522	g151490	7.00E−90	twitching motility
							protein
38	94750	31720	32301	MCA100523	g454838	7.00E−51	ORF 6; putative
38	94750	32364	33974	MCA100524	g1653472	e−120	NH(3)-dependent NAD(+)
							synthetase
38	94750	25258	27037	MCA100546	g2735093	0	ubiquitous surface
							protein A 2
38	94750	27198	28070	MCA100547	g2677632	1.00E−66	methionine regulatory
							protein MetR
38	94750	28330	28986	MCA100548	g1799710	3.00E−47	dedA protein
38	94750	70429	71286	MCA100628	g669111	9.00E−79	alternate atpB CDS
38	94750	71347	71586	MCA100629	g1573462	1.00E−14	ATP synthase F0,
							subunit c (atpE)
38	94750	71683	72144	MCA100630	g581814	4.00E−30	uncF (AA 1-156)
38	94750	72160	72699	MCA100631	g48336	9.00E−26	uncH (AA 1-177)
38	94750	72749	74284	MCA100632	g1790172	0	membrane-bound ATP
							synthase, F1 sector,
							alpha-subunit
38	94750	74372	75238	MCA100633	g1790171	3.00E−96	membrane-bound ATP
							synthase, F1 sector,
							gamma-subunit
38	94750	75694	77103	MCA100635	g1573457	0	ATP synthase F1,
							subunit beta (atpD)
38	94750	77188	77586	MCA100636	g1573456	2.00E−16	ATP synthase F1,
							subunit epsilon (atpC)
38	94750	42399	43304	MCA100808	g1788771	1.00E−66	orf, hypothetical
							protein
38	94750	23867	24892	MCA101243	g1573514	e−106	O-sialoglycoprotein
							endopeptidase (gcp)
38	94750	29005	29400	MCA101264	g1033113	1.00E−11	ORF_o113
38	94750	4673	5742	MCA101528	g216509	3.00E−82	cell division protein
							fstZ
38	94750	5866	6756	MCA101529	g1574235	1.00E−42	conserved hypothetical
							protein
38	94750	7767	8792	MCA101531	g440089	e−137	RecA
38	94750	9699	11027	MCA101533	g3876615	e−112	Similar to Yeast D-
							lactate dehydrogenase
							(SW: DLD1_YEAST)
38	94750	11050	11592	MCA101534
38	94750	11674	12723	MCA101535
38	94750	12838	13641	MCA101536	g1573029	1.00E−27	conserved hypothetical
							protein
38	94750	13667	14434	MCA101537	g1789177	1.00E−42	putative enzyme
38	94750	14676	15545	MCA101538	g1574480	e−101	2,3,4,5-
							tetrahydropyridine-2-
							carboxylate N-
							succinyltransf
38	94750	16830	17747	MCA101540	g1572971	3.00E−93	lipoate biosynthesis
							protein A (lipA)
38	94750	18269	19222	MCA101542	g1786681	2.00E−89	ferrochelatase: final
							enzyme of heme
							biosynthesis
38	94750	19956	21070	MCA101544	g1652222	9.00E−44	hypothetical protein
38	94750	21261	23480	MCA101545	g1030696	0	isocitrate
							dehydrogenase
38	94750	44197	46308	MCA101565	g1574600	9.00E−78	guanosine-3′,5′-
							bis (diphosphate) 3′-
							pyrophosphohydrolase
38	94750	46693	46932	MCA101566	g1574602	1.00E−14	DNA-directed RNA
							polymerase, omega
							chain (rpoZ)
38	94750	47038	47643	MCA101567	g290498	2.00E−50	5′ guanylate kinase
38	94750	47816	48742	MCA101568	g216456	e−110	hypothetical 34.8 K
							protein(PIR: JE0403)
38	94750	48853	50493	MCA101569	g1789259	e−124	ssDNA exonuclease,
							5′-> 3′ specific
38	94750	50589	51176	MCA101570	g290496	2.00E−33	o223
38	94750	51346	52017	MCA101572	g2984272	3.00E−19	hypothetical protein
38	94750	52519	53892	MCA101574	g2340815	0	L-2,4-
							diaminobutyrate: 2-
							ketoglutarate 4-
							aminotransferase
38	94750	54051	55967	MCA101575	g4454667	e−134	methyltransferase
38	94750	55995	58601	MCA101576	g4454668	0	restriction
							endonuclease
38	94750	58652	60190	MCA101577	g893355	0	L-2,4-diaminobutyrate
							decarboxylase
38	94750	60278	62041	MCA101578	g472402	e−128	UVR excinuclease
							subunit C
38	94750	62223	62858	MCA101579	g1573552	2.00E−44	phosphoglycolate
							phosphatase (gph)
38	94750	63199	63741	MCA101580
38	94750	63889	64746	MCA101581	g1786337	1.00E−42	putative tRNA
							synthetase
38	94750	64772	65185	MCA101582	g1786338	4.00E−43	dnaK suppressor
							protein
38	94750	65335	66003	MCA101583	g882562	1.00E−23	icc gene product
38	94750	66160	66916	MCA101584	g1573380	3.00E−27	conserved hypothetical
							integral membrane
							protein
38	94750	66967	67674	MCA101585	g1736501	1.00E−47	Sulfate transport ATP-
							binding protein CYsA.
38	94750	67700	68140	MCA101586	g1790480	7.00E−20	putative regulator
38	94750	69471	69878	MCA101588
38	94750	75267	75602	MCA101681
38	94750	68546	69241	MCA101853	g1788164	3.00E−16	putative adhesin
38	94750	34301	34576	MCA101890
38	94750	35674	36312	MCA101892
38	94750	87827	89506	MCA101940	g409365	0	urocanase
38	94750	89601	91106	MCA101941	g151274	e−164	histidine ammonialyase
							(hutH) precursor
							(gtg start codon (E. C.
							4.3.1.3)
38	94750	91634	92272	MCA101942	g149204	5.00E−35	histidine utilization
							repressor G
38	94750	92575	93723	MCA101946	g4106576	e−109	ORF9, highly similar
							to imidazolone
							propionate hydrolase
38	94750	15658	16503	MCA101947	g2285919	1.00E−13	K5L + K6L
38	94750	6816	7307	MCA101948	g1321618	6.00E−16
38	94750	80209	81537	MCA101953	g3402275	1.00E−51	EnvZ protein
38	94750	85007	87612	MCA101955	g2367097	0	aconitate hydrase B
39	100848	79190	79684	MCA100004	g1835603	1.00E−30	15 kDa protein
39	100848	77575	78220	MCA100013	g49095	2.00E−47	triosephosphate
							isomerase
39	100848	33560	34450	MCA100033	g1786984	3.00E−38	putative
							transcriptional
							regulator LYSR-type
39	100848	16050	17411	MCA100152	g154205	e−139	phosphomannomutase
39	100848	38007	39128	MCA100236	g1574558	2.00E−27	conserved hypothetical
							protein
39	100848	39149	40258	MCA100237	g1790713	7.00E−15	orf, hypothetical
							protein
39	100848	13324	14526	MCA100260	g1788092	4.00E−39	putative amino
							acid/amine transport
							protein
39	100848	14586	15035	MCA100261
39	100848	15091	15930	MCA100262	g1773171	4.00E−38	similar to M.
							tuberculosis
							MTCY277.09
39	100848	36123	37547	MCA100305	g2984771	e−101	PhpA
39	100848	34625	35815	MCA100306	g409800	e−132	tyrosine
							aminotransferase
39	100848	89115	89381	MCA100389	g429056	1.00E−26	ribosomal protein S15
39	100848	89607	91682	MCA100390	g3650364	0	polyribonucleotide
							nucleotidyltransferase
39	100848	91827	92300	MCA100391	g2959336	4.00E−46	hypothetical protein
39	100848	92532	92957	MCA100392	g1100876	5.00E−19	hypothetical OrfY
39	100848	92969	93382	MCA100393	g1789538	2.00E−08	orf, hypothetical
							protein
39	100848	93467	94066	MCA100394	g1789540	1.00E−06	putative periplasmic
							protein
39	100848	28411	29109	MCA100525	g41638	3.00E−64	PufX protein
39	100848	30030	30761	MCA100527	g1742082	8.00E−54	Internalin B
39	100848	30895	32214	MCA100528	g537059	e−129	ORF_f447
39	100848	32302	33378	MCA100529	g2916960	2.00E−46	chaA
39	100848	94363	94614	MCA100761	g415661	4.00E−14	putative; ORF3
39	100848	94621	95874	MCA100762	g415662	e−141	UDP-N-
							acetylglucosamine 1-
							carboxyvinyl
							transferase
39	100848	95992	96555	MCA100763	g2636005	8.00E−43	ATP
							phosphoribosyltransferase
39	100848	96820	98121	MCA100764	g2983343	e−101	histidinol
							dehydrogenase
39	100848	98225	99295	MCA100765	g440346	3.00E−99	histidinol phosphate
							aminotransferase
39	100848	99499	100359	MCA100766	g2984079	1.00E−41	fumarate hydratase
							(fumarase)
39	100848	79796	81271	MCA100801	g1789560	e−128	transcription pausing;
							L factor
39	100848	81439	84168	MCA100802	g3850831	0	initiation factor IF2-
							alpha
39	100848	86548	86931	MCA100804	g606107	2.00E−17	P15B
39	100848	86964	87845	MCA100805	g1574748	2.00E−54	tRNA pseudouridine 55
							synthase (truB)
39	100848	67997	69420	MCA100815	g717082	e−139	glutamyl-tRNA
							synthetase
39	100848	69744	70682	MCA100816	g42318	8.00E−73	orfB
39	100848	70742	71092	MCA100817
39	100848	71246	73027	MCA100818	g840842	2.00E−81	penicillin-binding
							protein 3
39	100848	73207	74637	MCA100819	g1574688	2.00E−74	UDP-N-acetylmuramyl-
							tripeptide synthetase
							(murE)
39	100848	74755	76140	MCA100820	g1786274	9.00E−76	D-alanine: D-alanine-
							adding enzyme
39	100848	76209	77270	MCA100821	g1574690	e−105	phospho-N-
							acetylmuramoyl-
							pentapeptide-
							transferase E
39	100848	18959	19780	MCA100862	g1789144	2.00E−46	orf, hypothetical
							protein
39	100848	19920	20072	MCA100863	g973208	4.00E−09	unknown
39	100848	20368	21621	MCA100864	g3650360	3.00E−58	polynucleotide
							adenylyltransferase
39	100848	22089	22535	MCA100865	g1573012	4.00E−30	2-amino-4-hydroxy-6-
							hydroxymethyldihydropteridine-
							pyroph
39	100848	22769	23563	MCA100866	g3970812	2.00E−74	3-methyl-2-
							oxobutanoate
							hydroxymethyltransferase
39	100848	23576	24412	MCA100867	g854607	2.00E−64	putative pantoate —
							beta-alanine ligase
39	100848	24556	25401	MCA100868	g4138364	3.00E−59	ORF284
39	100848	25460	26035	MCA100869	g4467403	2.00E−23	hsdS protein (AA 1-410
39	100848	26235	26776	MCA100870	g4155604	4.00E−16	putative
39	100848	29173	29787	MCA100902	g606319	7.00E−20	27 kD protein in
							ECDAMOPRA
39	100848	155	772	MCA100959
39	100848	787	1221	MCA100960
39	100848	2287	2865	MCA100962	g1789409	3.00E−18	orf, hypothetical
							protein
39	100848	3088	4974	MCA100963	g4176381	0	topoisomerase IV
							subunit
39	100848	5074	5685	MCA100964	g2622643	3.00E−33	imidazoleglycerol-
							phosphate synthase
39	100848	5692	6273	MCA100965	g38667	3.00E−57	hisB
39	100848	6509	7017	MCA100966	g41474	2.00E−43	fms
39	100848	7147	8805	MCA100967	g1800021	2.00E−69	DNA repair protein
							RecN
39	100848	8859	9404	MCA100968	g1789317	1.00E−30	orf, hypothetical
							protein
39	100848	9428	9826	MCA100969	g1789318	1.00E−23	orf, hypothetical
							protein
39	100848	9901	10368	MCA100970
39	100848	10483	10698	MCA100971	g1789881	1.00E−15	orf, hypothetical
							protein
39	100848	10775	11650	MCA100972	g2645800	3.00E−62	site-specific
							recombinase
39	100848	17947	18870	MCA100983	g1781241	1.00E−99	cysK
39	100848	27386	27973	MCA100985	g1814074	1.00E−34	DsbA
39	100848	40307	41437	MCA101057	g1657573	3.00E−49	hypothetical protein
39	100848	41491	41649	MCA101058
39	100848	41663	42544	MCA101059	g1773136	2.00E−52	acyl-coA thioesterase
							II
39	100848	42892	45303	MCA101060	g1573755	e−124	glycerol-3-phosphate
							acyltransferase (plsB)
39	100848	45434	46276	MCA101061	g3372537	1.00E−61	UTP-glucose-1-
							phosphate
							uridylyltransferase
39	100848	46369	47937	MCA101062	g927386	e−163	glucose-6-phosphate
							isomerase
39	100848	48368	48901	MCA101063	g3559950	1.00E−20	UDP-glucose 6-
							dehydrogenase
39	100848	49598	49843	MCA101064
39	100848	50331	50846	MCA101065
39	100848	64882	65763	MCA101402	g2661442	4.00E−80	YafJ
39	100848	62805	63572	MCA101404	g38674	2.00E−91	cyclase
39	100848	62144	62566	MCA101405	g1773099	2.00E−42	probable riboflavin
							synthase beta chain
39	100848	61547	61969	MCA101406	g1574763	4.00E−17	N utilization
							substance protein B
							(nusB)
39	100848	60480	61445	MCA101407	g2329840	1.00E−50	thiamine-monophosphate
							kinase
39	100848	59736	60230	MCA101408	g1574765	4.00E−19	phosphatidylglycerophosphatase
							A (pgpA)
39	100848	58735	59224	MCA101410	g2769574	4.00E−22	methylase
39	100848	56628	57614	MCA101412	g580766	1.00E−54	BepI modification
							methylase (AA 1-403)
39	100848	54681	55580	MCA101414	g1573822	8.00E−37	conserved hypothetical
							protein
39	100848	52655	54490	MCA101415	g2654003	0	glucosamine synthase
39	100848	51555	52574	MCA101416	g1429254	e−111	UDP-glucose 4-
							epimerase
39	100848	11886	13143	MCA101479	g1787337	e−109	3-oxoacyl-[acyl-
							carrier-protein]
							synthase II
39	100848	88447	88902	MCA101792	g940802	1.00E−15	outer membrane protein
39	100848	93930	94229	MCA101810
39	100848	50855	51313	MCA101869
39	100848	56357	56563	MCA101870
39	100848	63863	64879	MCA101871	g3089616	4.00E−13	homoserine kinase
							homolog
39	100848	65763	66659	MCA101872
39	100848	78259	78561	MCA102126
4	2642	463	783	MCA100115	g290546	1.00E−07	f135
4	2642	954	1610	MCA100117	g2960085	3.00E−15	hypothetical protein
							Rv3661
4	2642	1764	2642	MCA101198	g154276	8.00E−96	peptide chain release
							factor 2
40	119211	50160	50753	MCA100057	g4062767	2.00E−34	ZK688.3 protein
40	119211	50865	51788	MCA100058	g1359474	1.00E−81	homology to hydrolases
40	119211	51852	52013	MCA100059	g599606	5.00E−24	rubredoxin
40	119211	8413	8958	MCA100065	g4337446	1.00E−58	ECORLD_ORF1; encoded
							by M30388 and Z29635
40	119211	10888	11190	MCA100146	g1573418	2.00E−24	conserved hypothetical
							protein
40	119211	10282	10866	MCA100147	g1573419	2.00E−46	recombination protein
							(recR)
40	119211	9069	10181	MCA100148	g1788105	6.00E−35	RNase D, processes
							tRNA precursor
40	119211	106	690	MCA100179	g3861026	1.00E−13	unknown
40	119211	693	1781	MCA100180	g606171	6.00E−92	ORF_f375
40	119211	1850	2371	MCA100181	g1742876	3.00E−28	ORF_ID: o329#2; similar
							to [A40360]
40	119211	2693	3697	MCA100182	g2634701	1.00E−61	NAD (P) H-dependent
							glycerol-3-phosphate
							dehydrogenase
40	119211	7778	8185	MCA100367	g145892	2.00E−18	biotin carboxyl
							carrier protein
40	119211	6422	7750	MCA100368	g405541	e−152	biotin carboxylase
40	119211	5139	6181	MCA100369	g1786881	2.00E−94	putative ATP-binding
							protein in pho regulon
40	119211	4544	4891	MCA100370	g1786880	4.00E−13	orf, hypothetical
							protein
40	119211	27651	28547	MCA100431	g151405	e−111	phaseolotoxin
							sensitive octase
40	119211	26345	26839	MCA100433	g2632225	9.00E−15	YkuD protein
40	119211	76550	76939	MCA100482	g304913	3.00E−26	urf2
40	119211	114141	114743	MCA100510	g286176	7.00E−28	negative regulator of
							pyocin genes
40	119211	115659	116633	MCA100512
40	119211	116611	117456	MCA100513
40	119211	117460	118032	MCA100514
40	119211	22301	24235	MCA100948	g1574757	e−143	ABC transporter, ATP-
							binding protein
40	119211	21230	22201	MCA100949	g1872207	2.00E−35	HtrB homolog
40	119211	20793	21170	MCA100950	g2634659	4.00E−42	aspartate 1-
							decarboxylase
40	119211	17870	18673	MCA100952	g1052830	6.00E−63	indoleglycerol
							phosphate synthetase
40	119211	16782	17798	MCA100953	g143784	3.00E−42	tryptophanyl tRNA
							synthetase (EC
							6.1.1.2)
40	119211	15955	16656	MCA100954	g410131	8.00E−22	ORFX7
40	119211	15289	15762	MCA100955	g410132	3.00E−14	ORFX8
40	119211	14182	15102	MCA100956	g1574128	5.00E−73	conserved hypothetical
							protein
40	119211	77032	77787	MCA101016	g1573017	1.00E−50	tRNA delta(2)-
							isopentenylpyrophosphate
							transferase
40	119211	78161	78421	MCA101017	g1065627	3.00E−30	yersinia multiple
							regulator
40	119211	78982	79953	MCA101019	g1789588	4.00E−68	putative isomerase
40	119211	80020	80511	MCA101020	g2367202	6.00E−33	orf, hypothetical
							protein
40	119211	80545	81120	MCA101021
40	119211	81173	81667	MCA101023	g606139	6.00E−15	ORF_o185
40	119211	81698	82408	MCA101024	g2317737	3.00E−87	putative ABC
							transporter ATP-
							binding protein
40	119211	82528	86061	MCA101025	g2766693	0	proline dehydrogenase
40	119211	88029	89999	MCA101028	g1161059	3.00E−57	protease
40	119211	90522	92645	MCA101031
40	119211	60578	62242	MCA101150	g1574163	e−112	dihydrolipoamide
							acetyltransferase
							(aceF)
40	119211	48773	50050	MCA101214	g154288	e−142	5-
							phosphoribosylglycinamide
							synthetase
40	119211	47317	48624	MCA101215	g3087737	9.00E−44	ABC1 protein
40	119211	44031	44555	MCA101218	g1573090	1.00E−48	DNA polymerase III,
							epsilon subunit (dnaQ)
40	119211	43024	43593	MCA101220	g396335	3.00E−37	No definition line
							found
40	119211	42522	42941	MCA101221	g1742695	3.00E−34	Ferredoxin II.
40	119211	40605	40901	MCA101223	g1787504	7.00E−22	orf, hypothetical
							protein
40	119211	38672	40519	MCA101224	g1799717	7.00E−74	similar to [SwissProt
							Accession Number
							P44246]
40	119211	37107	37787	MCA101226	g3861231	6.00E−49	unknown
40	119211	114989	115282	MCA101355
40	119211	92788	93711	MCA101469	g1573776	e−104	cell division protein
							(ftsY)
40	119211	93897	94241	MCA101470	g2313803	2.00E−27	methylated-DNA -
							protein-cysteine
							methyltransferase
40	119211	94362	95357	MCA101471	g47870	2.00E−94	dihydroorotate oxidase
40	119211	95392	95904	MCA101472
40	119211	95970	97439	MCA101473	g1788651	e−171	amidophosphoribosyltransferase = PRPP
							amidotransferase
40	119211	97996	98835	MCA101475	g1944158	5.00E−36	lytic transglycosylase
40	119211	99306	101294	MCA101476	g1592818	0	uvrB
40	119211	101328	101969	MCA101477
40	119211	102078	105977	MCA101480	g1574781	2.00E−44	exodeoxyribonuclease
							V, beta chain (recB)
40	119211	106602	108041	MCA101482	g3142727	3.00E−49	exodeoxyribonuclease V
							subunit
40	119211	108251	109219	MCA101483	g3885440	1.00E−86	yhdG homolog
40	119211	109659	110585	MCA101484	g148275	5.00E−16	Exonuclease VII large
							subunit
40	119211	111005	111736	MCA101485	g2072699	4.00E−74	pvdS
40	119211	118395	118646	MCA101541
40	119211	118082	118393	MCA101543
40	119211	52375	53448	MCA101589	g151446	e−112	P-protein
40	119211	53505	54374	MCA101590	g410055	2.00E−43	cyclohexadienyl
							dehydrogenase
40	119211	54495	55763	MCA101591	g2634678	e−101	5-
							enolpyruvoylshikimate-
							3-phosphate synthase
40	119211	55862	56695	MCA101592	g1906367	4.00E−64	hypothetical protein
40	119211	56723	57088	MCA101593	g1789438	1.00E−10	putative kinase
40	119211	57079	57510	MCA101594
40	119211	57818	60442	MCA101595	g2564217	0	pyruvate dehydrogenase
							(lipoamide)
40	119211	62595	63365	MCA101597	g1789363	4.00E−78	orf, hypothetical
							protein
40	119211	67710	68651	MCA101599	g1788765	7.00E−77	thiosulfate binding
							protein
40	119211	69040	70197	MCA101600	g3978474	e−115	MetZ homolog
40	119211	70448	71575	MCA101601	g1574510	e−157	ribonucleoside
							diphosphate reductase,
							beta chain (nrdB)
40	119211	71681	71902	MCA101602	g1788568	2.00E−08	orf, hypothetical
							protein
40	119211	73244	74389	MCA101604	g498170	3.00E−87	carboxynorspermidine
							decarboxylase
40	119211	74602	75804	MCA101605	g1001125	3.00E−74	hypothetical protein
40	119211	75957	76511	MCA101606	g4155434	7.00E−36	putative
40	119211	112492	112878	MCA101770
40	119211	112942	113109	MCA101771
40	119211	118691	119050	MCA101772
40	119211	119052	119211	MCA101774
40	119211	18727	20568	MCA101814	g141801	1.00E−83	anthranilate
							phosphoribosyltransferase
							(EC 2.4.2.18)
40	119211	11382	13633	MCA101815	g1799581	0	ribonucleoside-
							diphosphate reductase
							1 alpha (EC1.17.4.1)
40	119211	63531	66164	MCA101886	g1573962	2.00E−39	exodeoxyribonuclease
							V, gamma chain (recC)
40	119211	44757	45182	MCA101959	g1552784	1.00E−34	ribonuclease H
40	119211	45397	45936	MCA101960	g3861372	2.00E−09	possible
							protoporphyrinogen
							oxidase (hemk)
40	119211	46032	47180	MCA101961	g2293312	3.00E−21	YtfP
40	119211	24876	26252	MCA101962	g598251	0	outer membrane protein E
40	119211	29114	29992	MCA101964	g2983572	5.00E−19	3-oxoacyl-[acyl-
							carrier-protein]
							synthase III
40	119211	31377	32036	MCA101965	g580875	3.00E−59	ipa-57d
40	119211	32139	32588	MCA101967	g1788911	3.00E−35	putative deaminase
40	119211	32677	33342	MCA101968	g1574149	2.00E−50	cytidylate kinase 1
							(cmkA)
40	119211	33597	35186	MCA101969	g1651439	0	30S ribosomal protein
							S1.
40	119211	35506	35781	MCA101970	g399670	2.00E−16	integration host
							factor beta subunit
40	119211	36355	37032	MCA101971	g805068	6.00E−56	OMP decarboxylase
40	119211	37969	38598	MCA101972	g2635898	2.00E−17	similar to
							hypothetical proteins
40	119211	86419	87177	MCA102059
40	119211	3811	4308	MCA102109	g1001123	6.00E−08	hypothetical protein
40	119211	24430	24660	MCA102111
40	119211	35812	36213	MCA102116
40	119211	30377	31330	MCA102117
41	269223	188318	189049	MCA100014	g2181957	5.00E−43	hypothetical protein
							Rv3300c
41	269223	77773	79113	MCA100035	g149757	0	outer membrane protein
							CD
41	269223	255725	256996	MCA100036	g882710	e−118	N-acetylglutamate
							synthase
41	269223	1764	2576	MCA100054	g1573276	2.00E−46	pyrroline-5-
							carboxylate reductase
							(proC)
41	269223	195583	196011	MCA100074	g1001829	4.00E−15	hypothetical protein
41	269223	82057	82719	MCA100076	g987642	5.00E−49	ribonuclease III
41	269223	79399	80121	MCA100078	g1788917	1.00E−61	pyridoxine
							biosynthesis
41	269223	127128	128444	MCA100098	g407186	3.00E−75	DnaA protein
41	269223	192138	192839	MCA100103	g2108342	1.00E−89	OmpR protein
41	269223	191142	192041	MCA100104	g1788499	6.00E−42	orf, hypothetical
							protein
41	269223	126337	126468	MCA100112	g147682	7.00E−16	ribosomal protein L34
41	269223	125896	126168	MCA100113	g581462	2.00E−13	homologous to E. coli
							rnpA
41	269223	125582	125788	MCA100114	g2898108	2.00E−15	9-10 kDa protein-like
41	269223	193168	195417	MCA100121	g1098475	e−171	region E; orf;
							homologous to E. coli
							o622, U18997
41	269223	254370	255644	MCA100131	g1574371	e−100	glutamate permease
							(gltS)
41	269223	4189	4955	MCA100190	g147322	2.00E−77	acetyl-CoA carboxylase
41	269223	41968	43620	MCA100198	g2367384	0	putative ATP-binding
							component of a
							transport system
41	269223	40805	41419	MCA100200	g2231726	2.00E−41	macrophage infectivity
							potentiator
41	269223	189796	190944	MCA100247	g1789473	e−107	putative transport
							protein
41	269223	185949	186641	MCA100307	g1574175	3.00E−48	16s pseudouridylate
							516 synthase (rsuA)
41	269223	184967	185572	MCA100308	g3135321	5.00E−12	putative
							thiol: disulfide
							interchange protein
							precursor
41	269223	183536	184672	MCA100309	g1389759	2.00E−94	DnaJ
41	269223	37916	38281	MCA100355	g3323226	2.00E−21	T. pallidum predicted
							coding region TP0895
41	269223	227863	230013	MCA100365	g391839	0	alpha-subunit of HDT
41	269223	230052	231215	MCA100366	g391840	e−146	beta-subunit of HDT
41	269223	36803	37561	MCA100439	g1468939	7.00E−60	meso-2,3-butanediol
							dehydrogenase (D-
							acetoin forming)
41	269223	34942	36237	MCA100441	g1657503	e−106	similar to S. aureus
							mercury (II) reductase
41	269223	33813	34805	MCA100442	g1001812	4.00E−72	hypothetical protein
41	269223	32952	33533	MCA100443	g1789819	2.00E−49	orf, hypothetical
							protein
41	269223	164675	165019	MCA100454	g2635307	3.00E−08	ysmA
41	269223	94670	95482	MCA100483	g1573330	e−120	iron (chelated) ABC
							transporter,
							periplasmic-binding
							prot
41	269223	95485	96356	MCA100484	g1573329	e−115	iron (chelated) ABC
							transporter, ATP-
							binding prot (yfeB)
41	269223	96387	97214	MCA100485	g1573328	e−100	iron (chelated) ABC
							transporter, permease
							prot (yfeC)
41	269223	97272	98081	MCA100486	g1245467	1.00E−87	YfeD
41	269223	231781	232396	MCA100534	g2340007	1.00E−28	YlbK protein
41	269223	233066	233581	MCA100536	g2342534	8.00E−45	PAPS reductase
41	269223	233689	234591	MCA100537	g1322409	9.00E−89	cysD
41	269223	234772	236025	MCA100538	g1322410	e−100	cysN
41	269223	236187	238250	MCA100539	g2367254	0	DNA helicase
41	269223	66114	68632	MCA100556	g1574437	e−153	cell division protein
							FtsK-related protein
41	269223	69114	69851	MCA100558	g2668599	2.00E−78	ATPase
41	269223	70011	70676	MCA100559	g1787088	8.00E−34	arginine 3rd transport
							system periplasmic
							binding prot
41	269223	70868	71533	MCA100560	g769794	2.00E−40	artJ
41	269223	75715	77502	MCA100597	g1790302	0	putative GTP-binding
							factor
41	269223	74090	75439	MCA100598	g1573640	e−127	UDP-N-
							acetylglucosamine
							pyrophosphorylase
							(glmU)
41	269223	73356	74006	MCA100599	g496542	1.00E−48	OccM
41	269223	71723	73317	MCA100600	g1787085	1.00E−36	arginine 3rd transport
							system periplasmic
							binding prot
41	269223	2850	4010	MCA100637	g971394	6.00E−27	similar to Acc. No.
							D26185
41	269223	176444	178372	MCA100657	g606286	e−158	ORF_o637
41	269223	179340	180227	MCA100659	g1789752	5.00E−45	orf, hypothetical
							protein
41	269223	180371	181150	MCA100660	g1185002	2.00E−47	dihydrodipicolinate
							reductase
41	269223	181240	182331	MCA100661	g304266	1.00E−45	cystathionine beta-
							lyase
41	269223	182445	183365	MCA100662	g2634328	3.00E−89	similar to sodium-
							dependent transporter
41	269223	178416	179237	MCA100692	g2293347	2.00E−12	DnaJ
41	269223	39931	40560	MCA100773	g451652	1.00E−45	unknown
41	269223	244876	245628	MCA101070	g4186118	2.00E−24	type 4 prepilin
							peptidase
41	269223	303	1001	MCA101092	g4155349	1.00E−27	phosphomethylpyrimidine
							kinase
41	269223	129669	130736	MCA101112	g150880	2.00E−37	putative
41	269223	82887	83588	MCA101125	g1788921	8.00E−43	leader peptidase
							(signal peptidase I)
41	269223	111855	112940	MCA101128	g150708	1.00E−99	[ribB] gene products
41	269223	268513	268884	MCA101181	g1224005	7.00E−40	ORF2; sim. to N-
							terminal
							phosphoribosyl c-AMP
							hydrolase
41	269223	268096	268443	MCA101182	g1224006	6.00E−28	ORF3; sim. to C-
							terminal
							phosphoribosyl c-AMP
							hydrolase
41	269223	267596	268026	MCA101183	g1224007	2.00E−18	ORF4
41	269223	266565	267230	MCA101184	g1224008	3.00E−59	ORF5; mutations in
							this gene affect the
							culture pH
41	269223	264696	266135	MCA101185	g2577963	5.00E−86	YerD protein
41	269223	263394	264128	MCA101187	g149205	6.00E−36	histidine utilization
							repressor C (hutC)
41	269223	260788	261690	MCA101189	g1573236	8.00E−61	conserved hypothetical
							protein
41	269223	259547	260607	MCA101190	g413953	1.00E−87	ipa-29d
41	269223	258434	259207	MCA101191	g413952	4.00E−45	ipa-28d
41	269223	44402	44662	MCA101279
41	269223	45635	47095	MCA101281	g1498192	8.00E−54	putative
41	269223	52663	52923	MCA101283	g1652924	3.00E−10	pterin-4a-
							carbinolamine
							dehydratase
41	269223	53084	55264	MCA101284	g4176379	0	topoisomerase IV
							subunit
41	269223	59095	59403	MCA101288
41	269223	59601	62384	MCA101289	g1573871	0	DNA polymerase I
							(polA)
41	269223	196489	197751	MCA101331	g141770	0	citrate synthase
							precursor
41	269223	250144	254073	MCA101372	g1788909	0	phosphoribosylformyl-
							glycine amide
							synthetase
41	269223	248757	249935	MCA101373	g2632881	1.00E−41	similar to
							bicyclomycin
							resistance protein
41	269223	246950	248584	MCA101374	g3220230	e−135	type IV pilus assembly
							protein TapB
41	269223	245649	246836	MCA101375	g3025702	1.00E−56	pilus assembly protein
							PilC
41	269223	244092	244709	MCA101377	g1573909	1.00E−33	conserved hypothetical
							protein
41	269223	240255	243272	MCA101379	g1736781	e−111	Acriflavin resistance
							protein D.
41	269223	239100	239612	MCA101381	g550460	4.00E−18	membrane fusion
							protein
41	269223	128505	129656	MCA101382	g45691	7.00E−61	dnaN protein (AA 1-367)
41	269223	131062	133455	MCA101384	g41646	0	gyrase B (AA 1-804)
41	269223	133644	135200	MCA101385	g1573186	0	GMP synthase (guaA)
41	269223	136888	137169	MCA101388	g1001663	2.00E−16	rare lipoprotein A
41	269223	137351	137692	MCA101389	g1652134	2.00E−23	FKBP-type peptidyl-
							prolyl cis-trans
							isomerase
41	269223	137915	139009	MCA101390	g2983314	3.00E−63	ornithine
							decarboxylase
41	269223	139063	140330	MCA101391	g1789996	4.00E−99	alanine-alpha-
							ketoisovalerate
							transaminase C
41	269223	140389	140727	MCA101392	g2407234	8.00E−26	similar to H.
							influenzae U32836
41	269223	140754	141998	MCA101393	g1787438	e−138	D-amino acid
							dehydrogenase subunit
41	269223	142379	144201	MCA101394	g1790427	0	thiamin biosynthesis,
							pyrimidine moiety
41	269223	144333	146159	MCA101395	g1574084	0	ABC transporter, ATP-
							binding protein
41	269223	146383	147726	MCA101396	g2635428	e−130	argininosuccinate
							lyase
41	269223	147971	148915	MCA101397	g41666	e−100	porphobilinogen
							deaminase (AA 1-313)
41	269223	149877	150605	MCA101399	g1573875	4.00E−46	conserved hypothetical
							protein
41	269223	38460	38705	MCA101530	g42543	1.00E−13	pspE protein
41	269223	31815	32798	MCA101546	g1001340	4.00E−54	hypothetical protein
41	269223	28035	30956	MCA101548	g4377308	e−118	Zinc Metalloprotease
							(insulinase family)
41	269223	26681	27871	MCA101549	g2367234	e−107	orf, hypothetical
							protein
41	269223	25873	26463	MCA101550	g1573078	1.00E−36	phosphatidylglycerophosphate
							synthase (pgsA)
41	269223	23781	24791	MCA101552	g1657863	0	NAD repressor/NMN
							transporter NadRp
41	269223	23259	23432	MCA101553	g2636024	5.00E−09	yvlC
41	269223	19781	22992	MCA101554	g1657862	0	glycyl-tRNA synthetase
							alpha subunit
41	269223	18833	19485	MCA101555	g1787111	1.00E−42	leucyl, phenylalanyl-
							tRNA-protein
							transferase
41	269223	17415	18665	MCA101556	g3284000	0	serine
							hydroxymethyltransferase
41	269223	16824	17255	MCA101557	g43231	1.00E−10	chorismate-pyruvate
							lyase
41	269223	14797	16386	MCA101558	g2662054	e−171	isocitrate lyase
41	269223	12474	14624	MCA101559	g1906369	0	hypothetical protein
41	269223	8656	11007	MCA101561	g1651530	e−160	Ribonuclease e (EC
							3.1.4.—) (RNase E).
41	269223	6766	7716	MCA101563	g1573385	5.00E−64	conserved hypothetical
							protein
41	269223	5116	6546	MCA101564	g4200042	e−112	exopolyphosphatase
41	269223	91641	91808	MCA101609	g208931	1.00E−16	ORF16-lacZ fusion
							protein
41	269223	88129	88366	MCA101611	g1334480	4.00E−14	unique orf
41	269223	86216	86662	MCA101614	g1573906	3.00E−65	H. influenzae
							predicted coding
							region HI0882
41	269223	83997	85778	MCA101615	g1572960	0	GTP-binding membrane
							protein (lepA)
41	269223	80995	81894	MCA101618	g1572957	1.00E−80	GTP-binding protein
							(era)
41	269223	175707	176225	MCA101619	g560723	5.00E−22	Mip = 24 kda macrophage
							infectivity
							potentiator protein
41	269223	174030	174176	MCA101621	g1894774	5.00E−16	rubredoxin
41	269223	172917	173972	MCA101622	g1789065	1.00E−42	putative
							oxidoreductase
41	269223	171413	172576	MCA101623	g2150108	2.00E−85	periplasmic substrate
							binding protein
41	269223	170503	171255	MCA101624	g2150109	5.00E−61	integral membrane
							protein
41	269223	169728	170423	MCA101625	g48972	2.00E−64	nitrate transporter
41	269223	169168	169497	MCA101626	g1574579	3.00E−30	conserved hypothetical
							protein
41	269223	167480	168979	MCA101627	g3005690	7.00E−91	gamma-glutamylcysteine
							synthetase
41	269223	165388	166755	MCA101629	g1573076	e−121	conserved hypothetical
							protein
41	269223	164248	164496	MCA101631	g1573769	9.00E−08	conserved hypothetical
							protein
41	269223	153230	153748	MCA101633	g1573022	8.00E−20	heat shock protein
							(grpE)
41	269223	151115	153019	MCA101634	g2522264	0	DnaK
41	269223	198632	198931	MCA101637	g2239247	1.00E−18	SdhC protein
41	269223	198958	199290	MCA101638	g42924	5.00E−19	succinate
							dehydrogenase
							hydrophobic subunit
41	269223	199379	201199	MCA101639	g3273345	0	fumarate reductase
							flavoprotein subunit
41	269223	201300	201977	MCA101640	g2239250	1.00E−96	succinate
							dehydrogenase putative
							iron sulphur subunit
41	269223	202407	205205	MCA101641	g39232	0	2-oxoglutarate
							dehydrogenase
41	269223	205326	206555	MCA101642	g39283	e−131	succinyltransferase
41	269223	206648	208090	MCA101643	g151345	e−155	dihydrolipoamide
							dehydrogenase
41	269223	212826	214043	MCA101645
41	269223	214142	215374	MCA101646
41	269223	216050	218155	MCA101648	g148698	3.00E−92	prolyl endopeptidase
41	269223	218735	220828	MCA101650	g1573174	e−147	oligopeptidase A
							(prlC)
41	269223	221075	221800	MCA101651	g1787008	8.00E−40	orf, hypothetical
							protein
41	269223	221952	222545	MCA101652	g882483	3.00E−50	ORF_o197
41	269223	222757	224055	MCA101653	g1773120	e−105	trigger factor
41	269223	224295	224885	MCA101654	g1773121	1.00E−84	ATP-dependent Clp
							proteinase
41	269223	224934	226208	MCA101655	g1573717	e−149	ATP-dependent Clp
							protease, ATP-binding
							subunit
41	269223	123662	125293	MCA101656	g45709	e−133	homologous to E. coli
							60 K
41	269223	122095	123465	MCA101657	g45710	e−113	homologous to E. coli
							50 K
41	269223	121548	121988	MCA101658	g42148	1.00E−46	orf1
41	269223	120490	121497	MCA101659	g581147	4.00E−80	orf2, homologue to
							B. subtilis ribG
41	269223	119545	120186	MCA101660	g150707	3.00E−49	riboflavin synthetase
							alpha subunit
41	269223	118437	119363	MCA101661	g3328155	4.00E−69	methionyl-tRNA
							formyltransferase
41	269223	117032	118369	MCA101662	g1573620	7.00E−65	sun protein (sun)
41	269223	115305	116708	MCA101663	g2160269	e−153	threonine synthase
41	269223	114048	115172	MCA101664	g1574014	2.00E−44	DNA processing chain A
							(dprA)
41	269223	113447	114028	MCA101665	g2367210	1.00E−19	orf, hypothetical
							protein
41	269223	110508	111677	MCA101668	g1460081	3.00E−85	hypothetical protein
							Rv2559c
41	269223	109304	109822	MCA101670	g402362	3.00E−15	hypothetical protein
41	269223	105340	106233	MCA101673	g1354827	3.00E−67	arginase
41	269223	104054	105262	MCA101674	g790956	e−145	ornithine
							aminotransferase
41	269223	103248	103808	MCA101675	g1628369	2.00E−10	gepB
41	269223	101499	102242	MCA101677	g4154851	3.00E−72	putative
41	269223	100074	101222	MCA101678	g1573761	2.00E−75	conserved hypothetical
							protein
41	269223	98638	99816	MCA101679	g1574452	e−120	tyrosyl tRNA
							synthetase (tyrS)
41	269223	44008	44328	MCA101794
41	269223	257352	257930	MCA101931
41	269223	238243	238896	MCA101934
41	269223	239645	239932	MCA101937
41	269223	243516	244079	MCA101943
41	269223	44993	45466	MCA101954
41	269223	186833	187384	MCA101958	g42358	5.00E−21	pepQ product, proline
							dipeptidase
41	269223	187980	188180	MCA101973	g3322357	1.00E−08	dnaK suppressor,
							putative
41	269223	211262	211762	MCA101976	g529727	7.00E−09	heme receptor
41	269223	55427	56215	MCA101978	g1788125	8.00E−47	putative enzyme
41	269223	56337	57158	MCA101979	g4155762	3.00E−16	putative
41	269223	57227	58789	MCA101980	g1574592	0	peptide chain release
							factor 3 (prfC)
41	269223	62725	65282	MCA101981	g1574197	0	DNA topoisomerase I
							(topA)
41	269223	106832	107182	MCA102132
41	269223	113110	113376	MCA102133	g1788096	5.00E−11	orf, hypothetical
							protein
41	269223	24857	25618	MCA102137	g1651338	7.00E−08	PnuC protein
41	269223	31241	31690	MCA102138
41	269223	135356	136573	MCA102139
41	269223	262656	262982	MCA102143
41	269223	148933	149691	MCA102146	g496215	5.00E−12	uropprphyrinogen-III-
							synthase
41	269223	155575	156525	MCA102147
41	269223	156368	159940	MCA102148
41	269223	160109	161479	MCA102149
41	269223	161476	162411	MCA102150
41	269223	162428	163453	MCA102151
41	269223	163450	164040	MCA102152

TABLE 2


Locus ID	End	Locus ID	End

MCA1c0001	5′	MCA1c0005	5′
MCA1c0001	3′	ND	ND
MCA1c0002	5′	ND	ND
MCA1c0002	3′	MCA1c0039	3′
MCA1c0003	5′	ND	ND
MCA1c0003	3′	ND	ND
MCA1c0004	5′	ND	ND
MCA1c0004	3′	MCA1c0009	5′
MCA1c0005	5′	MCA1c0001	5′
MCA1c0005	3′	ND	ND
MCA1c0006	5′	ND	ND
MCA1c0006	3′	MCA1c0033	5′
MCA1c0007	5′	ND	ND
MCA1c0007	3′	ND	ND
MCA1c0008	5′	ND	ND
MCA1c0008	3′	MCA1c0012	3′
MCA1c0009	5′	MCA1c0004	3′
MCA1c0009	3′	MCA1c0030	5′
MCA1c0010	5′	ND	ND
MCA1c0010	3′	ND	ND
MCA1c0011	5′	ND	ND
MCA1c0011	3′	ND	ND
MCA1c0012	5′	ND	ND
MCA1c0012	3′	MCA1c0008	3′
MCA1c0013	5′	ND
MCA1c0013	3′	ND
MCA1c0014	5′	ND
MCA1c0014	3′	ND
MCA1c0015	5′	ND
MCA1c0015	3′	MCA1c0026	5′
MCA1c0016	5′	MCA1c0019	3′
MCA1c0016	3′	ND
MCA1c0017	5′	ND
MCA1c0017	3′	ND
MCA1c0018	5′	MCA1c0038	3′
MCA1c0018	3′	MCA1c0021	3′
MCA1c0019	5′	ND
MCA1c0019	3′	MCA1c0016	5′
MCA1c0020	5′	ND
MCA1c0020	3′	ND
MCA1c0021	5′	ND	ND
MCA1c0021	3′	MCA1c0018	3′
MCA1c0022	5′	ND	ND
MCA1c0022	3′	ND	ND
MCA1c0023	5′	ND	ND
MCA1c0023	3′	ND	ND
MCA1c0024	5′	ND	ND
MCA1c0024	3′	ND	ND
MCA1c0025	5′	ND	ND
MCA1c0025	3′	ND	ND
MCA1c0026	5′	MCA1c0015	3′
MCA1c0026	3′	ND	ND
MCA1c0027	5′	ND	ND
MCA1c0027	3′	ND	ND
MCA1c0028	5′	MCA1c0029	3′
MCA1c0028	3′	ND	ND
MCA1c0029	5′	ND	ND
MCA1c0029	3′	MCA1c0028	5′
MCA1c0030	5′	MCA1c0009	3′
MCA1c0030	3′	ND	ND
MCA1c0031	5′	ND	ND
MCA1c0031	3′	ND	ND
MCA1c0032	5′	ND	ND
MCA1c0032	3′	ND	ND
MCA1c0033	5′	MCA1c0006	3′
MCA1c0033	3′	ND	ND
MCA1c0034	5′	MCA1c0036	3′
MCA1c0034	3′	ND	ND
MCA1c0035	5′	ND	ND
MCA1c0035	3′	ND	ND
MCA1c0036	5′	ND	ND
MCA1c0036	3′	MCA1c0034	5′
MCA1c0037	5′	ND	ND
MCA1c0037	3′	ND	ND
MCA1c0038	5′	ND	ND
MCA1c0038	3′	MCA1c0018	5′
MCA1c0039	5′	ND	ND
MCA1c0039	3′	MCA1c0002	3′
MCA1c0040	5′	ND	ND
MCA1c0040	3′	ND	ND
MCA1c0041	5′	ND	ND
MCA1c0041	3′	ND	ND

[0147]

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SEQUENCE LISTING

The patent application contains a lengthy “Sequence Listing” section. A copy of the “Sequence Listing” is available in electronic form from the USPTO

web site (http://seqdata.uspto.gov/sequence.html?DocID=20040067554). An electronic copy of the “Sequence Listing” will also be available from the

USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).

Claims

What is claimed is:

1. A purified or isolated nucleic acid consisting essentially of a nucleotide sequence that encodes the same UDP-N-acetylmuramoylalanine-D-glutamate ligase encoded by nucleotides 11357 to 12736 of SEQ ID NO:35 or a nucleotide sequence fully complementary thereto.

2. The purified or isolated nucleic acid of claim 1, wherein said nucleic acid sequence consists essentially of nucleotides 11357 to 12736 of SEQ ID NO:35 or a nucleotide sequence fully complementary thereto.

3. A purified or isolated oligonucleotide consisting essentially of a fragment of a nucleic acid having the nucleotide sequence of nucleotides 11357 to 12736 of SEQ ID NO:35 or a sequence complementary thereto, wherein said oligonucleotide is at least 22 nucleotides in length.

4. A recombinant construct comprising a nucleotide sequence that encodes the same UDP-N-acetylmuramoylalanine-D-glutamate ligase encoded by nucleotides 11357 to 12736 of SEQ ID NO:35, or a nucleotide sequence fully complementary thereto, operably linked to a promoter.

5. A method of making UDP-N-acetylmuramoylalanine-D-glutamate ligase of Moraxella catarrahalis comprising:

obtaining a nucleic acid consisting essentially of a nucleotide sequence that encodes the same UDP-N-acetylmuramoylalanine-D-glutamate ligase encoded by nucleotides 11357 to 12736 of SEQ ID NO:35;

inserting said nucleic acid in an expression vector such that said nucleic acid is operably linked to a promoter; and

introducing said expression vector into a host cell whereby said host cell produces the protein encoded by said nucleic acid.

6. The method of claim 5, further comprising isolating the protein.

7. The method of claim 5, wherein said nucleic acid sequence consists essentially of nucleotides 11357 to 12736 of SEQ ID NO:35 or a nucleotide sequence fully complementary thereto.

8. A method for constructing a host cell that expresses UDP-Nacetylmuramoylalanine-D-glutamate ligase of Moraxella catarrahalis comprising introducing a recombinant construct comprising a promoter operably linked to a nucleic acid comprising a nucleotide sequence that encodes the same UDP-N-acetylmuramoylalanine-D-glutamate ligase encoded by nucleotides 11357 to 12736 of SEQ ID NO:35 into said cell.

9. The method of claim 8, wherein said nucleic acid sequence consists essentially of nucleotides 11357 to 12736 of SEQ ID NO:35 or a nucleotide sequence fully complementary thereto.

10. A vector comprising the purified or isolated nucleic acid of claim 1

11. The vector of claim 10, wherein the isolated nucleic acid is operably linked to a promoter.

12. The vector of claim 11, wherein the vector is an expression vector.

13. A cultured cell line comprising the vector of claim 10.

14. A vector comprising the purified or isolated nucleic acid of claim 2.

15. The vector of claim 14, wherein the isolated nucleic acid is operably linked to a promoter.

16. The vector of claim 15, wherein the vector is an expression vector.

17. A cultured cell line comprising the vector of claim 14.

18. An isolated expression construct comprising nucleotides 11357 to 12736 of SEQ ID NO:35, which encodes UDP-N-acetylmuramoylalanine-D-glutamate ligase, or a nucleotide sequence fully complementary thereto, operably linked to a promoter.

19. A purified or isolated nucleic acid consisting essentially of a nucleic acid sequence which hybridizes under high stringency to nucleotides 11357 to 12736 of SEQ ID NO:35 and which encodes UDP-N-acetylmuramoylalanine-D-glutamate ligase.

20. A purified or isolated nucleic acid which hybridizes substantially over the entire length to nucleotides 11357 to 12736 of SEQ ID NO:35 or a sequence complementary thereto under the following conditions: 5×SSC with 1% SDS at 60° C.; and washing with 0.2×SSC with 0.1% SDS at either 45 C or 68° C. or 0.5M sodium phospahate (pH 7.2), 7% SDS, and 1 mM EDTA at 65° C.; and washing with 40 mM sodium phosphate, 1% SDS, 1 mM EDTA at 65° C.